gentoo resync : 15.12.2019

66 files changed, 147 insertions, 841 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 673f0b84cafd..1b6cf94f7c86 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/ariadne/Manifest b/sci-biology/ariadne/Manifest
deleted file mode 100644
index a6d67664e4fe..000000000000
--- a/sci-biology/ariadne/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-AUX ariadne-1.3-gcc4.patch 207 BLAKE2B 28c92410a33cd08da76de7631a64f21f65a4e576ec0fdfceb29a3f8c315b6eb083e613f8001c18c5f777f0a7e772af8cbebbbd5640144ea0cc9e5188d6e11f39 SHA512 81750d979dbabe25867daba2dd658eeb1a8e1c04560d2fc067ece20dc3e92abaf98aceefd769c79be87bfcfb18902cb2042a3abbf9c47f79ff281a02b0a9d249
-AUX ariadne-1.3-implicits.patch 480 BLAKE2B 5ff0117339e47bb3b0076f1db5a58d1f55bbaed7522615e5f60a85fea6da5aa48fe04f6550cf16b001c949c9f203a5c01f6fa3109ba4f4b2a327f04e81eab4cc SHA512 014dddcf7c3c107ecd77acb9d0110c50bf864cfa20959283ae868a74116d333e2a09749291882f12fffaabed34773e52c9cba5d0b7e476d1e8a14a7df5091a84
-DIST ariadne-1.3.tar.Z 69427 BLAKE2B 97277e78a2f8c2fd70117f40159d1c47b6c0e2b2c2b491dcc22b50d9842da128aeb3a03ec501d97391c38b8bfcdc3a903fa07770bf1030e5a46247ea14733cc4 SHA512 6c803f945bbcf36c08407e907ad716dc7cd01c7bed555777af46a5dc626b56ca3d1de7d16cab82bfa8bd5a91e06f42c590c0489594251405999459459e9c7289
-EBUILD ariadne-1.3-r3.ebuild 904 BLAKE2B b5f9b5240d431a690509c10016b2377ce8cfb491789b011b2ff2effab857d3127cb6ab7cdf0043e30f9eec0e3b868017f945ba9805eb1823ab63b900cdfdeb5e SHA512 eceba1b9bf54353df40f061deaa6925034d4bf029a735adce713e20a93a014fc921bfe50cd1caf1befce59348d7f15cbb5d4fe52f220534b05d8c1b3592adaf6
-MISC metadata.xml 954 BLAKE2B 1e8f172511ca1a79f772edf35f8a5fbae6c7530f75cfaca3a0b1e2e2ce724818ee8dc7e2545305cee9d75bb91ca777fe6da4db4b13bfcd318bb8dffa7210bdc0 SHA512 07101ae5c65d25810f0b32e5bef44b2ee078e858e17ee4b1351f444dc95ad746417f3684206c94487c6203bfcdafc5b0c67b17a1fb5fbfd4ba7a74009bfd2743
diff --git a/sci-biology/ariadne/ariadne-1.3-r3.ebuild b/sci-biology/ariadne/ariadne-1.3-r3.ebuild
deleted file mode 100644
index 0103c6d3648c..000000000000
--- a/sci-biology/ariadne/ariadne-1.3-r3.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-DESCRIPTION="Protein sequences and profiles comparison"
-HOMEPAGE="http://www.well.ox.ac.uk/ariadne/"
-SRC_URI="http://www.well.ox.ac.uk/${PN}/${P}.tar.Z"
-
-LICENSE="ARIADNE"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="static-libs"
-
-DEPEND=">=sci-biology/ncbi-tools-0.20041020-r1"
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}/SRC-${PV}
-
-PATCHES=(
-	"${FILESDIR}"/${P}-gcc4.patch
-	"${FILESDIR}"/${P}-implicits.patch
-)
-
-src_prepare() {
-	default
-	sed -i -e "s/\$(CFLAGS)/\$(LDFLAGS) &/" Makefile || die #359045
-	sed -e "s/blosum62/BLOSUM62/" -i prospero.c || die
-}
-
-src_compile() {
-	emake CC="$(tc-getCC)" OPTIMISE="${CFLAGS}"
-}
-
-src_install() {
-	dobin Linux/{ariadne,prospero}
-
-	use static-libs && dolib.a Linux/libseq.a
-
-	insinto /usr/include/${PN}
-	doins Include/*.h
-
-	einstalldocs
-}
diff --git a/sci-biology/ariadne/files/ariadne-1.3-gcc4.patch b/sci-biology/ariadne/files/ariadne-1.3-gcc4.patch
deleted file mode 100644
index 8bda75cb4f3a..000000000000
--- a/sci-biology/ariadne/files/ariadne-1.3-gcc4.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- a/cl.c
-+++ b/cl.c
-@@ -658,6 +658,7 @@
-       fclose(fp);
-       if ( ! stat( filename, &buf ) )
- 	{
-+	  char *ctime(), *t;
- 	  sprintf( date, "%s", ctime(&buf.st_mtime) );
- 	  t = date;
- 	  while ( *t )
diff --git a/sci-biology/ariadne/files/ariadne-1.3-implicits.patch b/sci-biology/ariadne/files/ariadne-1.3-implicits.patch
deleted file mode 100644
index 31c442b12265..000000000000
--- a/sci-biology/ariadne/files/ariadne-1.3-implicits.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-topalign.c:96:5: warning: implicit declaration of function ‘toupper’
-prospero.c:63:3: warning: implicit declaration of function ‘strcpy’
-
---- SRC-1.3/prospero.c
-+++ SRC-1.3/prospero.c
-@@ -26,6 +26,7 @@
- */
- 
- #include<stdio.h>
-+#include<string.h>
- #include<math.h>
- #include"cl.h"
- #include"seq_util.h"
---- SRC-1.3/topalign.c
-+++ SRC-1.3/topalign.c
-@@ -26,6 +26,7 @@
- */
- 
- #include<stdio.h>
-+#include<ctype.h>
- #include<math.h>
- #include"seq_util.h"
- #include"ariadne.h"
diff --git a/sci-biology/ariadne/metadata.xml b/sci-biology/ariadne/metadata.xml
deleted file mode 100644
index d0e8e0be55e0..000000000000
--- a/sci-biology/ariadne/metadata.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-		ARIADNE is a package of two programs, ariadne and prospero, that
-		compare protein sequences and profiles using the Smith-Waterman
-		algorithm, and assesses statistical significance using a new accurate
-		formula, described in Mott, 2000, "Accurate Formula for P-values of
-		gapped local sequence and profile alignments" J. Mol Biol. 300:649-659.
-		The sequence/profile comparison algorithms used in ARIADNE are
-		standard, and are probably not the fastest implementations available.
-		The novel part is the method for determining statistical significance,
-		which will give thresholds of significance that are accurate to within
-		5% 95% of the time.
-	</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest
index 8090dd7eaab3..f34306941b84 100644
--- a/sci-biology/augustus/Manifest
+++ b/sci-biology/augustus/Manifest
@@ -1,4 +1,4 @@
 AUX augustus-2.5.5-sane-build.patch 5271 BLAKE2B 1ba799aa4d9611087f1455f334dc35616979267bb546aa2ab16f6c8d3d528af84373da482840b455d4d0f0374af24cc3010f6925d4a93c0eb7abe524544fd408 SHA512 5afe12b51b8ce27ef32e8e66dd72be451022757228b4c86dec938b26870885bee06712438a22801a42944d2def8ae8bf4a2d7fdb82e12455c145abcd6f0c4aa1
 DIST augustus.2.5.5.tar.gz 70826249 BLAKE2B 3f3f1537c5c614f00298e1835eeb7bbe968987c3e0dee13299e1e26b4abf198d8635a93121b11722d2c90b63ff54cf153c72716d01c3ca033481bb54357b7bcf SHA512 33eb05d5c90200d2fc17026743d3a25e73aa3e217b8546f0bed4c94bcb460597d853377a67896e52e45ead5d736d13ed3b2c91b31fed8216da2920c825e8c20f
-EBUILD augustus-2.5.5.ebuild 1010 BLAKE2B 4c1e6fd9b147423f33a430395d98b228504eb8a1836f7da5e9e88348e94c356cf52a228ff43978e858a82f48e5d75cbc1d58f18ba20f7459920259191da12a2f SHA512 6cf6076dd9c1c957302f5ec65867b9055a29e4a893f925bc18cb96cc7c57509e65497013e574a33dbe718f0aeb4a25422078874cf0b85603b30ca40abe81527f
+EBUILD augustus-2.5.5.ebuild 910 BLAKE2B 5cde42582b4873dbaabe4457a4b7b4f5305b928cbfd7afc3c067cbeb3ea042e82faa56810b4f72078d57f7b0ecd4c96eaa30cfde5ef73d67c26fd05d0035d84e SHA512 03103b4d5cec5dfd46971f1a089d0c02d3cc5ecf7647ee5589e8e297b3f60689c2c763b8c8f2137becfa0e11c0e3c7977186c466085c3065f88eaf5a469bcb9c
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/augustus/augustus-2.5.5.ebuild b/sci-biology/augustus/augustus-2.5.5.ebuild
index ff4dfd6cc7e0..5bf36e85cb9b 100644
--- a/sci-biology/augustus/augustus-2.5.5.ebuild
+++ b/sci-biology/augustus/augustus-2.5.5.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=4
+EAPI=7
 
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="Eukaryotic gene predictor"
 HOMEPAGE="http://augustus.gobics.de/"
@@ -15,30 +15,31 @@ KEYWORDS="amd64 x86"
 IUSE="examples"
 
 S="${WORKDIR}/${PN}.${PV}"
+PATCHES=( "${FILESDIR}"/${P}-sane-build.patch )
 
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-sane-build.patch
+src_configure() {
 	tc-export CC CXX
 }
 
 src_compile() {
-	emake clean && emake
+	emake clean
+	default
 }
 
 src_install() {
 	dobin bin/*
-#	dobin src/{augustus,etraining,consensusFinder,curve2hints,fastBlockSearch,prepareAlign}
 
 	exeinto /usr/libexec/${PN}
 	doexe scripts/*.p*
+
 	insinto /usr/libexec/${PN}
 	doins scripts/*.conf
 
 	insinto /usr/share/${PN}
 	doins -r config
 
-	echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > "${S}/99${PN}"
-	doenvd "${S}/99${PN}"
+	echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > 99${PN} || die
+	doenvd 99${PN}
 
 	dodoc -r README.TXT HISTORY.TXT docs/*.{pdf,txt}
 
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
index 4c404331ab52..5ceccbec9fa5 100644
--- a/sci-biology/bedtools/Manifest
+++ b/sci-biology/bedtools/Manifest
@@ -1,4 +1,4 @@
 DIST bedtools-2.26.0-fix-buildsystem.patch.bz2 2584 BLAKE2B 550cd03a0c01217adb347587cb75bdc2ffa4e03ad6ad66535b22d423e6f030e237b0ccfd3d1bd3e434cb9cc2a007971517f03e9ceabc08b63c725bac786e23e8 SHA512 0a7835f560102ce6183736faea6a2be05609b69bb8efdaf98b9d7057e24aa1ebe9d6067118b95c76470ca341b151970db532094ee70ca333075aed7c47509ba3
 DIST bedtools-2.26.0.tar.gz 19939711 BLAKE2B 8f6ee6ed755c638dbdd0a4750a5348c28a865f36eaafef6160e90f62912cb0a6b719713935ba68dad74bc591e3f37db49eab54a06a316dc00e4ec82a5dca71dc SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def
-EBUILD bedtools-2.26.0.ebuild 942 BLAKE2B ad27f9a2e62216a68c07dd0021f72240b7a1c296b87b13d49adb38e2bff050b8ef82dbe9d1e0cb81bcd9402915e7f33cbda10902748aae707e780cb177268e07 SHA512 61a3b76cfa50463cc49e58dbeccb3cbdf2d7315b780547ae323c7298a1a422a016bed044be21dfc5711c1393db135426ce72f49a048cf41bb9e3c780692bb0dd
+EBUILD bedtools-2.26.0.ebuild 969 BLAKE2B 325dee5796741cfc37c28cde5a3202665ed9d4f66c5a5d6ce2e798126e46e5f22799ad4daaaa1fe94cf98302a7b1cb12f7d4d50c7c446f4d3da32f35e422f8cb SHA512 f7b320772c9f0cb99011e08bdcb9238757c11f31784c9b9bdf6f43498fd416dde3fb5cd617d7821b059c2d7f484a1bf379ddcba9cf634f61ab80eb5fa73b842a
 MISC metadata.xml 761 BLAKE2B 35d57919e32a4b8bd6070ab5a513f62578394d43098d9e7b9b0765fd57d684c049dad9ec1b315044518bf01535d505e9d9d3fee540308df40c0b70886db8e49f SHA512 2d98b9559ef00bee2b741f9e7d22645442ba161f3cadb32c6366b39fcd71b6eac52afd210f59ae709a15cba36a2d0a47341345740e0cab6a1f6bfdffed064770
diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild
index c759b395f587..0705d9f46645 100644
--- a/sci-biology/bedtools/bedtools-2.26.0.ebuild
+++ b/sci-biology/bedtools/bedtools-2.26.0.ebuild
@@ -16,6 +16,7 @@ LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="test"
+RESTRICT="!test? ( test )"
 
 DEPEND="${PYTHON_DEPS}
 	test? (
diff --git a/sci-biology/bfast/Manifest b/sci-biology/bfast/Manifest
index 056c9ee88283..d9ec14eacea8 100644
--- a/sci-biology/bfast/Manifest
+++ b/sci-biology/bfast/Manifest
@@ -1,3 +1,3 @@
 DIST bfast-0.7.0a.tar.gz 2456617 BLAKE2B a841e7651e731dbb3faf22eb03dce5d2008c84f9a6198204d3c41aea26626058e3a23375bc0e7e8fc142d4898e09ddbb168016c71a7b79527e602e06ec329151 SHA512 16e7ec5101c478f0dfc171016cbacb2b9240773e43b2d40eeb42d0e47afcee50a6dd5838e043a0326fc1ca9a87d3e55b42326a7f17b7c5654ef9825913860836
-EBUILD bfast-0.7.0a.ebuild 878 BLAKE2B 7c1c986d2ac817f88bb22b1fd63cf8e66cc8e6ef45c3ec0cf4aff426891be864d5502d07deaf41f0d319a0ca07766a69a33f25a2ea1af72e28edd329c3415524 SHA512 1250f77e618c3164126e584cb85efec65afb4a8884ea30c8b4418ee812907824945bbc945893e48eb45c21ee3b082efb235616c891507c3494e81341c804693c
+EBUILD bfast-0.7.0a.ebuild 902 BLAKE2B c5e520867849c07323fd6002cc881160272259f4b002320453b1e529daeb9b89125da9b51f640bd708cad2f9fbc092dc5e5cb957803e5926a0eee2de18f87e7b SHA512 0807ad435ef822c9697b812b8bfec37fe2aaf701a6e60fac1dd15de821686d94101240cc70b829d46627dfbb0fe3e158ea0daeb873c54ff1f8b594a61be3ffbc
 MISC metadata.xml 346 BLAKE2B cf096d053302cd40548e541557cbe72f41e81328a93b41a6e19ae88122e9939d5e6414eb6f60ee6e96411f43a073151f7d98ab780858afa16c50c1a5e37f2c48 SHA512 b402eeeb37be04022693af8692b128bb257a69b8eeb75170506352fe05fa6e7154c908267bbab7af7d38d1eee26ad6d98e6be5f9c8647181aa491b3fb1680b62
diff --git a/sci-biology/bfast/bfast-0.7.0a.ebuild b/sci-biology/bfast/bfast-0.7.0a.ebuild
index 33fc6b8ef8b0..97282d2244a4 100644
--- a/sci-biology/bfast/bfast-0.7.0a.ebuild
+++ b/sci-biology/bfast/bfast-0.7.0a.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -14,6 +14,7 @@ SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
 LICENSE="GPL-2"
 SLOT="0"
 IUSE="test"
+RESTRICT="!test? ( test )"
 KEYWORDS="~amd64 ~x86"
 
 DEPEND=""
diff --git a/sci-biology/biopandas/Manifest b/sci-biology/biopandas/Manifest
index 078e8397d3a2..2d7765d9adbc 100644
--- a/sci-biology/biopandas/Manifest
+++ b/sci-biology/biopandas/Manifest
@@ -1,3 +1,3 @@
 DIST biopandas-0.2.1.tar.gz 209379 BLAKE2B 839a6f569f12b95c9b1c75dc755d009c77d7ef8224e517aed5026ffa6c33bd3826fe3862fec03469e967005a500600782fc372951d61358e2fe3bb56af734228 SHA512 0ea7aec84251d8d6ec4736c4968228133bd8622afb17d6916287168cb9f9757c5a97a4d5a52ac0e2f30027bf0edf9d76413db142f70d606f1359b8a4e06de7c8
-EBUILD biopandas-0.2.1.ebuild 1061 BLAKE2B adc9dcd6248cf5a720efd53a0db7d64701ece870fe4f851210d312aff1f8ccea29187bdb732254f80b2bfbbd6acc24ea7f5f74f4b5c1fb7798170c894e6eb455 SHA512 af6888f773aca4c9e93ea53de9861542398d952bab8f817cae9dba2b6613a993f051c260e7aa0a6919644561cc0f37df466a5e23b3d8fb727f674ee38e49a0c9
+EBUILD biopandas-0.2.1.ebuild 1088 BLAKE2B 8cc423a572181b72e827aa8a84b85fa37aed8db08036f80fd3ca12acc3cb0960a8529dffc94b26eb25c56a250a805f79eec759c8888905a672ec349a3198f973 SHA512 f3af16a98f8fa984a95678a894775b7eb2581ec9bf6e38beaf0e343410ab8f118a5d2f34b6d32fee3c12fde0c322b4d55daa68756888a6d9681081baa17c709b
 MISC metadata.xml 536 BLAKE2B e3cb776d0332fff486a7e1ea1353c54694ff687d4685bbb51728db0ed2025bb3d09d39cf7c9ea9f11546cbf9c4727661348e2f5fdfc13ffac2329ef6dfbe7450 SHA512 502803e30ecfac53516b56501a7bffeb49c3c0bc44ce5b3dd87aac5c745de614c235523ba3be374fcbede1a9a7bcf11c328abb27d82e087b275303f38b80b166
diff --git a/sci-biology/biopandas/biopandas-0.2.1.ebuild b/sci-biology/biopandas/biopandas-0.2.1.ebuild
index 4260d0a440a1..bbbd43d92d26 100644
--- a/sci-biology/biopandas/biopandas-0.2.1.ebuild
+++ b/sci-biology/biopandas/biopandas-0.2.1.ebuild
@@ -21,6 +21,7 @@ LICENSE="BSD"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="test"
+RESTRICT="!test? ( test )"
 
 RDEPEND="
 	dev-python/numpy[${PYTHON_USEDEP}]
diff --git a/sci-biology/bioperl-network/Manifest b/sci-biology/bioperl-network/Manifest
index adea06031a36..916e8474b098 100644
--- a/sci-biology/bioperl-network/Manifest
+++ b/sci-biology/bioperl-network/Manifest
@@ -1,4 +1,4 @@
 DIST BioPerl-Network-1.006900.tar.gz 2198089 BLAKE2B 67197ed356f642d9e85f779019f6854f4baa3963e059895b89c75ae56f8b5a075ca04b04ce5c7622d46a3a2f55e1c7d80af695085c607ed7fda5517c71c579f3 SHA512 d0a95af17cb024cbc615c784f1dbcddd7bfc5b54524163ab127f1077ded18df222fe067c085f3dd17dd416d6417b8f726526be164e1e33144991393f6b6d5842
-EBUILD bioperl-network-1.6.9.ebuild 610 BLAKE2B a54745ebcc3c5b52a302d2086bf2d25f384aeaf074280320792ffbbc7b257559d3cbf20d17c6ad04035cb49eeddb22143ee9346cf2ad7bf770c2c9bfdeb25a81 SHA512 75a872e2925c8d7662caad9e68d490fb1be835ef26038aaf7520765c15ae87b64369d7123715e8182f3ee3a0017a441a45a869e743e6773162831e75b1ebe4c4
-EBUILD bioperl-network-9999-r1.ebuild 642 BLAKE2B 8a4120f8380b5fab4bc60cb20b97acae366acf5392e8716137e1c6fe90c9ad225558fa35fcfcd4c48cfbd94dc47c02ecc9ba27f6b587d6d7ebc207fe07720f48 SHA512 455ccb0f4b3b426d6930f2efed4771a2538afafe47141defec5532500ea75a2954bf4e71f39ec7a3229821e74dcf1aecdce370c5e05479e4317ebc2553936ab4
+EBUILD bioperl-network-1.6.9.ebuild 634 BLAKE2B 7cb788c94d5017434f0f81dc5adbd3d64c31980d12f4e739862fc5127dea25f40964f11b384d42e73022b3fa4031d69e78bcb9f8933bab867827144d83596a02 SHA512 491c8190c28b7add4c1263038534705a7798afd29fbdfc853267f4b663b1fd92c21acfe47330357b83323e4ac05e39e52f78fa526ae1ae0059701a002f7ce03c
+EBUILD bioperl-network-9999-r1.ebuild 666 BLAKE2B cc26881e82203bdf13a7fe04229ac57d5fa23271674502114d5fea0daf89a770fd906a9c20b64bef56bda392392d22090362707b32f7c0d466349c5ae8fb8545 SHA512 24829c8d9199b9d559e978c3187d0db950fb112b4f20152ec790133770de9aa173b596653322f0d670df366c8075f2ffe4bcd420204ed00f238b485d8621c323
 MISC metadata.xml 349 BLAKE2B 18f5a67acf0859a50cca897d39e3e1a200eba44198d5c2bb1176d29579dd97dfcaf8b2cb8ffa4baf9c2adc7072f24b0344701a986b7a4f5a8491cf85b4086579 SHA512 dc3b8e26619cb4ff0dffeb79aa91f402a35cb2f673ecfd0bdac9d3667be82c248dcdd246185a006e8b91c9b66157689eaaf8ee464e00c54227c2c78cd9827b63
diff --git a/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild b/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild
index f199589337d9..65a72e06634f 100644
--- a/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild
+++ b/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI="5"
@@ -16,6 +16,7 @@ HOMEPAGE="http://www.bioperl.org/"
 SLOT="0"
 KEYWORDS="amd64 x86"
 IUSE="test"
+RESTRICT="!test? ( test )"
 SRC_TEST="do"
 
 CDEPEND=">=sci-biology/bioperl-${PV}
diff --git a/sci-biology/bioperl-network/bioperl-network-9999-r1.ebuild b/sci-biology/bioperl-network/bioperl-network-9999-r1.ebuild
index 19dc6f7d52e4..6be8f1cd8509 100644
--- a/sci-biology/bioperl-network/bioperl-network-9999-r1.ebuild
+++ b/sci-biology/bioperl-network/bioperl-network-9999-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI="5"
@@ -14,6 +14,7 @@ LICENSE="Artistic GPL-2"
 SLOT="0"
 KEYWORDS=""
 IUSE="test"
+RESTRICT="!test? ( test )"
 SRC_TEST="do"
 
 CDEPEND=">=sci-biology/bioperl-${PV}
diff --git a/sci-biology/exonerate/Manifest b/sci-biology/exonerate/Manifest
index ac1ad5a16b05..edfda5895233 100644
--- a/sci-biology/exonerate/Manifest
+++ b/sci-biology/exonerate/Manifest
@@ -1,4 +1,4 @@
 AUX exonerate-2.2.0-asneeded.patch 362 BLAKE2B 57bb7d7d57bf2347fc0cb20f650cd0a452bd70ed8ed46a87d132cf8d68e152438ec2c4e877129feb91748f5ca43021cc0010cf2f50b3bdb8eed60218d904eb27 SHA512 7c08fe7ee520ab7198557f5ac7f99f0bae53da77d46949d6bac78a3330fc9023a4aece085e060ad6a40303475999654dcfe5311d3a78f1d1be0d461cefbfcfb0
 DIST exonerate-2.2.0.tar.gz 509870 BLAKE2B 58b12338ef7d819a8e33ab87d72afe807ca219581a8f35ae38951860915a676bb9ba34a481f685e970948d9272be3e5f28d6b63c14f4d5facf35c4be52530d3b SHA512 c0aec4df83fbf6bcd1b27242397349769211ab88d71e2d081e20cb5453a03acd805807535a69841e991cf543d99fcd458cbd22d60b21f0fc6ce813eac45b838c
-EBUILD exonerate-2.2.0-r2.ebuild 943 BLAKE2B 7671c56095f96f92562690260d66551df961b01e5467ce6766b44255ff67ad11effc0e8f131c3b47e64152d77ad4792c41a4ad8b293342685d17709355d97499 SHA512 830ed336dd8bb4cf59fb59099d968459530fe37ae8b1874d535dadf4d3874410592d28049abbc8dd0e66ccc4e277cd7855602dcc42e7ac61394249557cf033a2
+EBUILD exonerate-2.2.0-r2.ebuild 967 BLAKE2B 27a48f5dc4e1040f4296152ae445ba6bb2dc29132605b6cce240c40d2719d16c0c7d80103d2b9f8440fb7d5bb8fec3e8ba0385f6f87b9196b443dd14ae1a6310 SHA512 1d5be70396afabf08489501cba460bb47a7bfe9efead75226b07707ed00813f0dcd69611b75e3135444ee100ceeaf2cd492cd79ffc5f3d01e6f5d808ce84f2e1
 MISC metadata.xml 438 BLAKE2B ae3dbc6cf8628225e3238076ec24fbadffd60818cb051cfc153c37af4cadbce7070697f0a2f21219a5a32aa9ebe8e4518fb2e4eb0e147959965f468fb0629b2d SHA512 e77d02d4d9664234895ef29ffc633e2e8ae49ac8c324fe0e82ac6ec3ac416570443f4a9831838d2eceb420398dfb5c5872b562861002974fa8754b2d846cf777
diff --git a/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild b/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild
index dcd09feac3d9..53ae5a97c6ae 100644
--- a/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild
+++ b/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -13,6 +13,7 @@ LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~ppc-macos ~x64-macos"
 IUSE="test threads utils"
+RESTRICT="!test? ( test )"
 REQUIRED_USE="test? ( utils )"
 
 DEPEND="dev-libs/glib:2"
diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest
index 587682895717..3a6a9eddf1fd 100644
--- a/sci-biology/fasta/Manifest
+++ b/sci-biology/fasta/Manifest
@@ -1,4 +1,4 @@
 AUX fasta-36.3.5e-ldflags.patch 2781 BLAKE2B e6d4e0984b4dadfc9d38504ab215d769084edc6c79cfe641b6b3fba8264a40add1665027295ec4afa19d26277036bfe1a5103ecdf72ef91a1139542ac8272954 SHA512 5424bb8385def72ff75701c2da153f697520cbec82f36cbed8de0e98f93d399de660e79da7700ab0ff688fd5388cf9f42a30ccc4359335ae02042bf8cbb3aae7
 DIST fasta-36.3.5e.tar.gz 943763 BLAKE2B 6234d0aee76af6614e6d25ebcfbdfae080db5bc5adf611aeb6edc53ed7c6cb6cef257bf852ed39bc286527cec4175c251765ce23ea5ff39d12ff8947dba97ac6 SHA512 ddfcae36dadd7e2ed5c8c8c0bda2eed077e9f6cd55e4ebf507690671af156358e9da4e7cb1406d2b8713c326c54a9d829fc25e668b16dfa6df48d18e3a009812
-EBUILD fasta-36.3.5e.ebuild 1626 BLAKE2B 0227b1f5b986e3155ef64637ed8dcac75bf92e9ec0e36320a0c43e89cd160fec87f59c16796bc4621f96b2df68082d3ebb2a2b33fb024c10544c45fd9680e358 SHA512 06ebb5136e78c0cf34ba2145aeda1a21e979b09ac53acfa8ad91c161dea363791d5e9b9b4a26b02111e7e6f1131c03fdd7a12e66ddcbf16e360540893abcf721
+EBUILD fasta-36.3.5e.ebuild 1643 BLAKE2B 43c8f7f4d2220aa7c028bba399241f0f024faa78b6743178793f647f6b494c749fb5ccb164cd07071b2ba28cfd60e61c75bb46c5f23556de131df5f0be60616b SHA512 caffe54bbfd73f76e3ef9adff0843103362f3945986a4b51ac722a8ea893de24994142e0995c13d9d1e6d846547a37427b643b11d04794f815a162d3ea03bef0
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/fasta/fasta-36.3.5e.ebuild b/sci-biology/fasta/fasta-36.3.5e.ebuild
index 30fda7e9ae00..392ee4c76410 100644
--- a/sci-biology/fasta/fasta-36.3.5e.ebuild
+++ b/sci-biology/fasta/fasta-36.3.5e.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -13,6 +13,7 @@ LICENSE="fasta"
 SLOT="0"
 KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 IUSE="debug cpu_flags_x86_sse2 test"
+RESTRICT="!test? ( test )"
 
 DEPEND="test? ( app-shells/tcsh )"
 RDEPEND=""
@@ -66,7 +67,7 @@ src_install() {
 
 	pushd bin > /dev/null || die
 	for bin in *36; do
-		dosym ${bin} /usr/bin/${bin%36} || die
+		dosym ${bin} /usr/bin/${bin%36}
 	done
 	popd
 
diff --git a/sci-biology/gibbs/Manifest b/sci-biology/gibbs/Manifest
index 3a203ab08d5a..e806435c017b 100644
--- a/sci-biology/gibbs/Manifest
+++ b/sci-biology/gibbs/Manifest
@@ -1,3 +1,4 @@
+AUX gibbs-3.1-fix-CFLAGS.patch 213 BLAKE2B 9a0f7f0412569cef1cce984f5087f7b99e16163ac6c6c3e0aad27f14cd2f7ed5bfb22f21f433f1c343a9e73899dedb00ea93467adc4cc42a3dceae41aa1e3f86 SHA512 afd0fffb891eefe8799025a032a802f398ac737900e1fac86f79964bfe493ee906c3e5f42abc5e45d3de5af80887ab25ef207a885a6ddb8b6fe0d0ab1f906046
 DIST gibbs-3.1.tar.gz 563300 BLAKE2B 74b97407ccdac49d19dd2fa5fe3a5384b52a3ae871f197c1212e818fb7ce2307f2d04a91cf8a1d14c82d57b6f7266bbae849091bec9e580b8d473b595a836212 SHA512 b1ffc0d0c7debaced3c3d850eb7d2c42e13358d1e7c6ff5e6be0273446edc50bd655c52c5ae904a9054d47d7a48abd54a7684534ba7681375b657ad77fb8cb52
-EBUILD gibbs-3.1.ebuild 1080 BLAKE2B 8b300d04feca4973c43a787410f19ff6ab78f5bb18d7e073cedc88c9c4c96b476d27a487a3b5d64ded499ac1ae60a21659e4023fba7d4a62368fbf05882edc33 SHA512 d07fc647931b6d8c0634a4d089429fade0f3d3262e0369236420963ba7dd6e3450a66cc0d4fe3ecc884a67e6aba8322d3492fc7a8b7a9fa8b32813e3973bc1fb
+EBUILD gibbs-3.1.ebuild 912 BLAKE2B 29d51a769e6a477bb81da6d467a1b2befbfd2f83282184a1087de0a4a5d736a5df01f3767663141bd6282826bd4fcad5ca0ddaea916fc93e582ccd8b4a8e98b8 SHA512 975c0bd3c57a8db25324636ce8f2fd9ef9bde1de4a980ba93fbe3e7bf8362a51f06ae5b1687570d81012ef6eed6536bfde418327a045bcf54a1e1517d85d989f
 MISC metadata.xml 483 BLAKE2B e5a503d65b225af960b42424b1e2e451ed0596240e15868f04c429920a7818333819abbb21b0340cd4ec9ddbcc23cc272663bc8451fd1ab11bf6d6f17e4eae2f SHA512 3f86f0f0f673f78c65187f282c0346fccab1102a01869811afd73a6070a3efa032ff9d427a57a9e8a9922cdc055a33d6bccb771eda1196d6667b3076035fd077
diff --git a/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch b/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch
new file mode 100644
index 000000000000..6eaad637cfc8
--- /dev/null
+++ b/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch
@@ -0,0 +1,11 @@
+--- a/configure.in
++++ b/configure.in
+@@ -51,7 +51,7 @@
+ 	fi

+ 	])

+ 

+-CFLAGS="$OPTFLAGS $MPIFLAGS  -Wall -Werror $MACFLAG"

++CFLAGS="$CFLAGS $OPTFLAGS $MPIFLAGS -Wall $MACFLAG"

+ 

+ AC_PROG_CC([$COMP_LIST])

+ 

diff --git a/sci-biology/gibbs/gibbs-3.1.ebuild b/sci-biology/gibbs/gibbs-3.1.ebuild
index de8322a5068e..a06d0880ee4d 100644
--- a/sci-biology/gibbs/gibbs-3.1.ebuild
+++ b/sci-biology/gibbs/gibbs-3.1.ebuild
@@ -1,11 +1,9 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=4
+EAPI=7
 
-AUTOTOOLS_AUTORECONF=yes
-
-inherit autotools-utils multilib
+inherit autotools
 
 DESCRIPTION="Identify motifs, conserved regions, in DNA or protein sequences"
 HOMEPAGE="http://bayesweb.wadsworth.org/gibbs/gibbs.html"
@@ -13,37 +11,37 @@ SRC_URI="mirror://gentoo/gibbs-${PV}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
-IUSE="mpi"
 KEYWORDS="amd64 x86"
+IUSE="mpi"
 
 DEPEND="
 	mpi? (
 		virtual/mpi
-		sys-cluster/mpe2 )"
+		sys-cluster/mpe2
+	)"
 RDEPEND="${DEPEND}"
 
+PATCHES=( "${FILESDIR}"/${PN}-3.1-fix-CFLAGS.patch )
+
 src_prepare() {
-	sed \
-		-e 's/CFLAGS="$OPTFLAGS/CFLAGS="$CFLAGS $OPTFLAGS/' \
-		-e 's/-Werror//' \
-		-i configure.in || die
-	autotools-utils_src_prepare
+	default
+	mv configure.{in,ac} || die
+	eautoreconf
 }
 
 src_configure() {
-	if use mpi; then export CC=mpicc; fi
-	local myeconfargs=( $(use_enable mpi) )
-	autotools-utils_src_configure
+	use mpi && export CC=mpicc
+	econf $(use_enable mpi)
 }
 
 src_install() {
-	autotools-utils_src_install
+	default
+
 	exeinto /usr/$(get_libdir)/${PN}
 	doexe *.pl
-	dodoc README ChangeLog
 }
 
 pkg_postinst() {
-	einfo "Supplementary Perl scripts for Gibbs have been installed into /usr/$(get_libdir)/${PN}."
+	einfo "Supplementary Perl scripts for Gibbs have been installed into ${EROOT}/usr/$(get_libdir)/${PN}."
 	einfo "These scripts require installation of sci-biology/bioperl."
 }
diff --git a/sci-biology/glimmerhmm/Manifest b/sci-biology/glimmerhmm/Manifest
index 24f25f908fc3..4de35b164fb1 100644
--- a/sci-biology/glimmerhmm/Manifest
+++ b/sci-biology/glimmerhmm/Manifest
@@ -1,4 +1,5 @@
 AUX 3.0.1-gentoo.patch 4235 BLAKE2B 8263516018df83c39da08e906bcdbfb8445ef26c064a82d8edf547fba5b569921905dd32476a99726f1864cc24ec5464fbc48db55e08cca0b9555647dddae120 SHA512 e0350a4b604fe76462bbb7139264a9b2916c050c335589031bdca0cf0c6a653bbf84d9827f5c2096ff13f1007d4ef2e93698814758f787a98e4dd818be44bc3d
+AUX glimmerhmm-3.0.1-fix-data-path.patch 512 BLAKE2B fc37954be58eaaec074fbb3ff9a8109907fc71be39365aa07e62c884a78c910d0ffcceaee907736107b56d97f0e7c9baf30f9fd71f239ede6cebe4bc9bcfb59e SHA512 0e1b65887a7a27c8d9adbf88a904ddbb4afc56e5052a6693ca57ae160bc9c6dab8589b633d364aead873fc1aaa671580bfc0deed9bde153f5069a0351244ef51
 DIST GlimmerHMM-3.0.1.tar.gz 45475952 BLAKE2B 355f4e9f26c31167e0935de8012fa99a243838d0dd47e0e46ae4cb1df4eaf188a13fb365025bc4be82805c89f36f534a9907030515f96b9422340e9e966f4ea6 SHA512 15307d1982527bd83433882552cd3e12c76a65a2a119b6911a748dc801f80b1fc5732cb769a52e5c6281bdd48cf619a02edbd1b96ee40319fc620a3a7cdd82b7
-EBUILD glimmerhmm-3.0.1-r1.ebuild 1190 BLAKE2B ab0c495ffc681f595d466b236826df1eea014424c8797013e9627cffc9cb1e37411955ebccadcaf0f678c13d159b32187b0f6e6a3f3ffdc572208c0e61c0d681 SHA512 9faea51c07ef865eb0dfd9028077ef7a3e42a633ca39dd1a66caf817a35a75236ecda3ed58f9941bd18c925f43a4319e65f1f03510032bfe92f0cae81076dd9d
+EBUILD glimmerhmm-3.0.1-r1.ebuild 989 BLAKE2B 7b411464fe1fd149ee78db9f067ff9c549854cf0ee8d572df30d0d03c3081bfe66c7ad26ad3051313909a51fc0ef0ac7e6e13f0ec378bf23929d2d4267d3b764 SHA512 1a55d81a6294016b4c90c952f49810ddf0a34f5b6b299f0040775a6a7cebe94aad5730d864143d4f09457b6616032fae2da3c893f47501d7c7effe60616a7196
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/glimmerhmm/files/glimmerhmm-3.0.1-fix-data-path.patch b/sci-biology/glimmerhmm/files/glimmerhmm-3.0.1-fix-data-path.patch
new file mode 100644
index 000000000000..3ad5090086eb
--- /dev/null
+++ b/sci-biology/glimmerhmm/files/glimmerhmm-3.0.1-fix-data-path.patch
@@ -0,0 +1,20 @@
+--- a/train/trainGlimmerHMM
++++ b/train/trainGlimmerHMM
+@@ -12,7 +12,7 @@
+ use Cwd;
+ 
+ use FindBin;
+-use lib $FindBin::Bin;
++use lib "/usr/share/glimmerhmm/lib";
+ use orf;
+ use formtrain;
+ use dectree_allinfo;
+@@ -20,7 +20,7 @@
+ use splitiso;
+ 
+ my $workdir=cwd();
+-my $scriptdir=$FindBin::Bin; # directory where all training programs should be
++my $scriptdir="/usr/libexec/glimmerhmm/training_utils"; # directory where all training programs should be
+ 
+ #print "workdir=$workdir scriptdir=$scriptdir\n";exit;
+ 
diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
index 1d3cf1171d76..5424e942a7f7 100644
--- a/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
+++ b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=4
+EAPI=7
 
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
 
 MY_P=GlimmerHMM
 
@@ -13,27 +13,22 @@ SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/${MY_P}-${PV}.tar.gz"
 
 LICENSE="Artistic"
 SLOT="0"
-IUSE=""
 KEYWORDS="amd64 x86"
 
-src_unpack() {
-	unpack ${A}
-	mv GlimmerHMM ${P}
-}
+S="${WORKDIR}/${MY_P}"
 
-src_prepare() {
-	sed \
-		-e 's|\(my $scriptdir=\)$FindBin::Bin|\1"/usr/libexec/'${PN}'/training_utils"|' \
-		-e 's|\(use lib\) $FindBin::Bin|\1 "/usr/share/'${PN}'/lib"|' \
-		-i "${S}/train/trainGlimmerHMM" || die
+PATCHES=(
+	"${FILESDIR}"/${PV}-gentoo.patch
+	"${FILESDIR}"/${PN}-3.0.1-fix-data-path.patch
+)
 
-	epatch "${FILESDIR}"/${PV}-gentoo.patch
+src_configure() {
 	tc-export CC CXX
 }
 
 src_compile() {
-	emake -C "${S}/sources"
-	emake -C "${S}/train"
+	emake -C sources
+	emake -C train
 }
 
 src_install() {
@@ -41,8 +36,10 @@ src_install() {
 
 	insinto /usr/share/${PN}/lib
 	doins train/*.pm
+
 	insinto /usr/share/${PN}/models
-	doins -r trained_dir/*
+	doins -r trained_dir/.
+
 	exeinto /usr/libexec/${PN}/training_utils
 	doexe train/{build{1,2,-icm,-icm-noframe},erfapp,falsecomp,findsites,karlin,score,score{2,ATG,ATG2,STOP,STOP2},splicescore}
 
diff --git a/sci-biology/hmmer/Manifest b/sci-biology/hmmer/Manifest
index a0715106c712..56d3862050f0 100644
--- a/sci-biology/hmmer/Manifest
+++ b/sci-biology/hmmer/Manifest
@@ -4,6 +4,6 @@ AUX hmmer-3.1_beta2-fix-header-install-path.patch 3202 BLAKE2B e6f8050c2edd11c89
 AUX hmmer-3.1_beta2-fix-perl-shebangs.patch 8605 BLAKE2B c0c78fed780b43df960dc24914e5dabe161243cec015deaf058d7eebf79c5e1633ded4f1305bb37b9766d74588009142fd58886e67810940e9601ef138647c21 SHA512 ce2c91c2d34d49dd5082a97ca0543bf3a176c792b4efd0cb37561114fc572b41d6cd546e16267283d33138ad54e2bb0c9c912c8fa1142e558a5452e9e72da2ff
 DIST hmmer-2.3.2.tar.gz 1024933 BLAKE2B 34fdc7b24b28d653022c80a63b2fd8376c15c961e1550a04cb310943d165575a2721cc5e4cb516335f57414f8621b7e62c4e30ee1f107bb714e40c59ed37d418 SHA512 5abf9c304de38b183a5beab7a5cfc75c3774ff6e161b7b8e55a0eae9fd156dbb7ed95d216c16d3c585c494bb69e3a9fdfabfb5dc729b7050a4d1be95c74df7d7
 DIST hmmer-3.1b2.tar.gz 5965253 BLAKE2B 38d1d6fb43aa814c0e3ddc551469ebd6b967f181c45df3802598f31abef10998595218167555a8862c0d2caa9118d9a7f1c22b673b6d596665f797ba903093f5 SHA512 64c8a840cb62160a1c13a20e64f42d297edb7969425d5047eefd8ee9f992d66612d62843523e8f33a2c38568ce1b0a9df23dd1d3ecf6773007f6db12d4cc4771
-EBUILD hmmer-2.3.2-r4.ebuild 1631 BLAKE2B 2d27ff5c3d172444c84aac4cae95b990f311ac28b9733fc30ed629c5b6cd03893bc07bea2b5ab4d722a1e6fe23f3d3ac5cb9b007c1fbacff63b40b0d33833664 SHA512 c237c12b1c8f0d3059055f361bd0d74aaf4997506e7ffce4ea52ba4f4ddaf96863df306f54192f42c209ca74c32d66c82ee0408c5cf44d15b774c83d2a38c188
-EBUILD hmmer-3.1_beta2.ebuild 1039 BLAKE2B 2533b7c77b156222a2c0171330addee16dd7ebb21bb9951aaeb8fa638631275737d3e9373e1225b16bb2e97023d5493690cad85abbc1d2dccce1f0e83753c976 SHA512 fdc4c77b49d32f5d767a351d09faca6c9229d0a58060514fcf9a455a50d6649b016d71269874e9de4ecd7a121a1bfa9c84f493641beb39f0da43d87155f15c6a
+EBUILD hmmer-2.3.2-r4.ebuild 1655 BLAKE2B ffc67289bc761e07d60df1d87e11abcc311b1fccc1652d542b71e0914660f3ed03e4a6e540d76d2c38e0d5cb43c606496da34fcac48bb84ee08c2a4822f0c562 SHA512 f07e067a72e388ebaff6c4712173bd6e68004a778c36823bcc685c7727a81ca77b448d046f2dec599b9c760b0c45fc379971beef227d2f6d43917a13e75b6abb
+EBUILD hmmer-3.1_beta2.ebuild 1063 BLAKE2B a3469ebea515d16eb960fb5021ae7374b8736dbc0e0e933146f570478bf24cbfcee2eef59008126315669ab67cd70b569ddf401e07dd78b15a96e8d6b4329296 SHA512 fa75524ced910f633735ab72a1eb8d0ae0fd3ccc88dc12f98995b546fdd5084158509c8c99fe231450f5151dacc2b9477ee35090d9657401e47f8bd1dd0240b6
 MISC metadata.xml 261 BLAKE2B 3768c926bca545090342a947ba83e706a8954c51b99a5e7b3476ba5198cd326fe1c3b8efb51dfd6be1800682556b8ceea065e388981463ab32f3d687951872f3 SHA512 537da0d3aa2741ebe4442d5dd9b53409decfc9d12ca8e5af8e737c4deb2910c884207e2d441025d19469816100889f04c11038bdffd6a1a15c6217495445090a
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild
index cd0e1d732b8b..a58b60f93288 100644
--- a/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild
+++ b/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -10,6 +10,7 @@ SRC_URI="http://eddylab.org/software/${PN}/${PV}/${P}.tar.gz"
 
 SLOT="2"
 IUSE="altivec test threads"
+RESTRICT="!test? ( test )"
 KEYWORDS="~amd64 ~x86"
 
 DEPEND="test? ( dev-lang/perl )"
diff --git a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild b/sci-biology/hmmer/hmmer-3.1_beta2.ebuild
index f94fcca8c295..b65fa0824f9b 100644
--- a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild
+++ b/sci-biology/hmmer/hmmer-3.1_beta2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -12,6 +12,7 @@ SRC_URI="http://eddylab.org/software/${PN}3/${MY_PV}/hmmer-${MY_PV}.tar.gz"
 LICENSE="GPL-3"
 SLOT="0"
 IUSE="altivec cpu_flags_x86_sse gsl mpi test +threads"
+RESTRICT="!test? ( test )"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
 
 RDEPEND="
diff --git a/sci-biology/last/Manifest b/sci-biology/last/Manifest
index 8ffbaad190ba..d2fab5c0d3f4 100644
--- a/sci-biology/last/Manifest
+++ b/sci-biology/last/Manifest
@@ -1,7 +1,5 @@
 AUX last-299-fix-build-system.patch 2021 BLAKE2B 6b2c1e5830c0076a444841c9740bba9bc5389dd1996efc2ca79989d61162f1594e46f0b7b982a7d50b25284e6394e0e427f7dfe3fc7cc22dbdc15d12f3f8a11c SHA512 42df26ce39dd8d263581f20aee0a3fbea0c849fcb5b1627554f9d0b3d3cea55a13b7f42fca9048611a50fdd9e784fa2b537a876b6ded411601c78b2e13e2e19c
 AUX last-299-portable-shebangs.patch 2762 BLAKE2B cb92f32c7118cca83114ffb534d0db04d258a63825592721eb80ed0a699aa9adfbe0df6eb0b33de8647e238b295103632333e89847b9a6b1b4bea9e940113316 SHA512 343483b421e79996aee5480608cdf8b085e8c9c48f5b1f6a6e6e6bbddca9f8d9e1e3561924bc29bc9c60f30cc4c5e7e81d79e60847e35b3a9f7a53f7e3b8c3f6
-DIST last-230.zip 418077 BLAKE2B 372dbf986ec926c91598085c579bc92d6449dfb6fbf6a240558514ce9d9efd4c3f8e26d17b78528d09afa182fd6e23713e639f3b02a4f4d639afa16fecb5f3a5 SHA512 46c858c2bd4a9aa00ac3b448ce78bdee6c1edd4f6569cff3c81ec8a7c661d89a9b5e7a888cbc6da190b243f0ec83c485b4574dadc6a58669d9b955eb70c329d1
 DIST last-299.zip 453159 BLAKE2B 3f8ddc24a2eba189880f2547f458ebbc2b349f0517c25165257f4cf3a90f68d8df313f7eece3930c33376aa0e16185c54b586b6f411975a1fb15e6426c535ca0 SHA512 74e89129cc17482ec1a99e2d940ca62374c130fea2fa53ea7d2c3703b6ca5751f348110909d61562c4839d8fb1793619c2f41c25c8968b3ab53f0c7191f4a00b
-EBUILD last-230.ebuild 710 BLAKE2B 23d3d780d35ff8bdd47f664d716acadaba66b3b29982cd5b9ebc4f12b99eb4207cfc2b7474f68a8d6bedc157f9e0d16548706d952b901902c0478822f67d6d4e SHA512 dc8a8ed6a4fd31daeb188cd79da40593e71ebbcc9567815ea4d445b033fe82ce6730af4e82cd9c2a5e17e07b97193b91ca2f034c636cfa7aae815208c1f3c591
 EBUILD last-299-r1.ebuild 843 BLAKE2B ce536c49888cb0ca7620c24f1767c95b99547f9b05f5dabe744884b6bb1b5f6c19ca3cb8697799ef0817720b52fab870ec508c70c82897bdf3581e05b16e3112 SHA512 7892c3a4ab3f6a23af11a5b548f4f7d992497c25bb4eed8e0a9dcac3da9b9a41d7b8f2b97f88599c7831fee5c064b421b0876fe0b3c444395015a4a0918f57e2
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/last/last-230.ebuild b/sci-biology/last/last-230.ebuild
deleted file mode 100644
index 29134bb908df..000000000000
--- a/sci-biology/last/last-230.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Genome-scale comparison of biological sequences"
-HOMEPAGE="http://last.cbrc.jp/"
-SRC_URI="http://last.cbrc.jp/archive/${P}.zip"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86"
-
-DEPEND="app-arch/unzip"
-RDEPEND=""
-
-src_prepare() {
-	sed \
-		-e 's:-o $@:$(LDFLAGS) -o $@:g' \
-		-i src/makefile || die
-}
-
-src_compile() {
-	emake \
-		-e -C src \
-		CXX="$(tc-getCXX)" \
-		CC="$(tc-getCC)" \
-		STRICT="" || die
-}
-
-src_install() {
-	dobin src/last{al,db,ex}
-	exeinto /usr/share/${PN}/scripts
-	doexe scripts/*
-	dodoc doc/*.txt ChangeLog.txt README.txt
-}
diff --git a/sci-biology/mcl/Manifest b/sci-biology/mcl/Manifest
index a92496d3dcc6..8bef0282bc82 100644
--- a/sci-biology/mcl/Manifest
+++ b/sci-biology/mcl/Manifest
@@ -1,8 +1,4 @@
 AUX mcl-14.137-qa-implicit-declarations.patch 786 BLAKE2B c7a5ed8f32dd3542766beaed19c9236a137444fdf69252becedfcc2d97136b0eba276355d2b24a38a06e0f78e6eaeb813bdc713cb01161167d4a2c65425e3c03 SHA512 e1388441e06075e951a1ff9994a8e9fe1083042c09e072c68e9abb20dc4a83498eb4cb71aa71d738268a50a0e03ee8e7976df9bbb304b8c90314d682bb8625d3
-DIST mcl-08-312.tar.gz 2749006 BLAKE2B ea575f0b436e42d69e9f66e1beef595503a5c56dce72b54c1095ce3225da1cee1820827bbaaa3fc39fa2ba1ce6aec115e8c4fe0b22a3212cce5e613ad33197d4 SHA512 9f89f81af398710ebb9135c93653d892fc9daef360d70f3b890a3133d8a17dddffe568b110d3370602cead895562bc0dc5a71020834b3b3e9b6d2abf4bf64b0b
-DIST mcl-12-135.tar.gz 2970824 BLAKE2B f70fd018cf0e1efba45abb9b3e0b09ce32026c255f6c58ffebc91059e2402231273d7b5956d97fe97e7509c5b90b98a86eaea30bb9a20955aed437871ef5d08b SHA512 97234e88f3430f223e1f303577b2b8853f40de6b204de415466719f691f529a795b17bf2fd48d4cc73d05900c87a10ba9afabbe54bce9367ee59215e7db0a8f5
 DIST mcl-14-137.tar.gz 3035491 BLAKE2B d6b975841a9094055306056ae0cd646cc92af69018893981d32b0604a583f61d3764bc67c1e21a0861b89a17013c01bcd4c1d7cbb4e0c5856403c2a767121423 SHA512 7e399e571de60da5e1ba9e643b7f0cd98fe484cc8cef517222a57322b5c7a04afa675c7cf0ab88b5801efa9565e5e67a14c4914987964308391d88dd4be1bea2
-EBUILD mcl-08.312.ebuild 678 BLAKE2B 2d616c862e2b4e8af4cb9e5534db8813c986e2ca4d26e3002ae92e36bf0e672339b5406b1a4808c60f28ea21237c622c64db1b70c5f9876ccd12cbc53501b354 SHA512 e628f2226efd505d191efdaac7a9f83e896d5b97455833aa7a6846fc7a8c8a1079fcc60fc343606252e839a3a2820dc6ab53ad84d57ae582f339b840bfbe9cc6
-EBUILD mcl-12.135.ebuild 678 BLAKE2B 2d616c862e2b4e8af4cb9e5534db8813c986e2ca4d26e3002ae92e36bf0e672339b5406b1a4808c60f28ea21237c622c64db1b70c5f9876ccd12cbc53501b354 SHA512 e628f2226efd505d191efdaac7a9f83e896d5b97455833aa7a6846fc7a8c8a1079fcc60fc343606252e839a3a2820dc6ab53ad84d57ae582f339b840bfbe9cc6
 EBUILD mcl-14.137.ebuild 651 BLAKE2B 73ba9d5ac8159a10ced22a9a39e0d5c1c4943fe5cc4ad1e823592e6362ef1f9bd3f850173a6e2c91d43bcfb825d3fd4de91dad469b27e58bd2a43c036889415f SHA512 042277297965d4796d0805dad2a951e8bd467630c7904fe1a5211616fc2a620c041ea6093bbaf10e6fed17037bccd7013afcfb0260e69c09bd1cdc3ca2f76f53
 MISC metadata.xml 336 BLAKE2B 077cf6e56ca5ba6480b00411536b1814f73b8dc93faf9337e0e81f3c47f174172894487ef072637dd396f39a95cd3a6538c2fd3e62328c3659882629c9b96dff SHA512 41ed664e2fdc26c5984fb55d90365cb02fe0de893d74e74935d2a9f6eb17e2e56a33210ed7d03c28375fb27ebbae3dca472de79a2e387ecf769a604aea629da3
diff --git a/sci-biology/mcl/mcl-08.312.ebuild b/sci-biology/mcl/mcl-08.312.ebuild
deleted file mode 100644
index fb0bf237a671..000000000000
--- a/sci-biology/mcl/mcl-08.312.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils
-
-MY_P="${PN}-${PV/./-}"
-
-DESCRIPTION="A Markov Cluster Algorithm implementation"
-HOMEPAGE="http://micans.org/mcl/"
-SRC_URI="http://micans.org/mcl/src/${MY_P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+blast"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	find \
-		-name Makefile.am \
-		-exec sed \
-			-e '/docdir/d' \
-			-e '/exampledir/s:doc::g' \
-			-i '{}' + || die
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=( $(use_enable blast) )
-	autotools-utils_src_configure
-}
diff --git a/sci-biology/mcl/mcl-12.135.ebuild b/sci-biology/mcl/mcl-12.135.ebuild
deleted file mode 100644
index fb0bf237a671..000000000000
--- a/sci-biology/mcl/mcl-12.135.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils
-
-MY_P="${PN}-${PV/./-}"
-
-DESCRIPTION="A Markov Cluster Algorithm implementation"
-HOMEPAGE="http://micans.org/mcl/"
-SRC_URI="http://micans.org/mcl/src/${MY_P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+blast"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	find \
-		-name Makefile.am \
-		-exec sed \
-			-e '/docdir/d' \
-			-e '/exampledir/s:doc::g' \
-			-i '{}' + || die
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=( $(use_enable blast) )
-	autotools-utils_src_configure
-}
diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest
index 258d6ba15b46..b934891dfcbd 100644
--- a/sci-biology/mira/Manifest
+++ b/sci-biology/mira/Manifest
@@ -3,5 +3,5 @@ AUX mira-4.0.2-cmath.patch 295 BLAKE2B 30892b3a519682db7e04b1a0169c4018d7f4dd4e3
 AUX mira-4.0.2-cout.patch 735 BLAKE2B d386a704829b7f3264ee69d55d7451a5479a9d121e49cbd8d9322c9a27a065073076608569d169982784fcc6cc4ae4423712d15d1c4d642a6b8fd0dd7d5fe3a3 SHA512 9d1aa493d20481d0a7e3eaefba36dc29d7903f70c9a445b6e0ea478d04124e8a81de37c437f0fb28c0a395562db7e78217cf09e500fd4a1f2a1f929c1d4d2a5a
 DIST mira-4.0.2.tar.bz2 10368046 BLAKE2B cc84c6c13c8024409634ccafd103be8a4f2a9e27fa7f19d2ef401393db9e8063a6fac2f21cd25dfe58e90aee8cf38983369d928241f9bc65e78da0e95fa41d3b SHA512 a7f9845de207cefb87ffa652f4f6b9b85735ef22eeb29b456e4d946ba1675e7dd2c78abb2da56f11fddcb699f5c0700a08ce298196ce1a8e586a758a8d3bdc7e
 DIST mira_3rdparty_06-07-2012.tar.bz2 31656 BLAKE2B 7e952d96e9073acd8ab1d1fc7c51c37f6526287d31698c5090500d421147285b535e8cab7e49f4e51a5634c901d1cd969206b1727e683d3fcebdc195399e3589 SHA512 4d4dbdf7ab5126f9d47160bee8bc127b6a225de8087f6b9914c754324a74d966333207c86a3f38cf0ea9f91408707e2a24086dbe1318fdfa2870b0c39bc5033b
-EBUILD mira-4.0.2.ebuild 2596 BLAKE2B 688e9bd306f0d99f3c5a28a406cbce9d8434ada339450a2b5f786a4775b4d45f728debf393ff1a158f37d0dbeaf49151fa021fa9d848b1a05d426837e4696775 SHA512 d39da2d62806f3d8efb5f998b363c7309d9e2254a3f084497e2fc7c86858804e55247b9deea1460b1c1dc017f7cf587174ee3c23ad62158d74c447de16bfae0a
+EBUILD mira-4.0.2.ebuild 2579 BLAKE2B 32dfbe06949674e8932bd87453bbfafe8b969f459f4512e82e92754e336673e588bee13bbcb6c95879c799a469adb8ce9894e18100e141acd11a28c85dcbf169 SHA512 94c1b9e0cf23495ef36ee9bec1aa4770e5d97011de06fc92f6b9d51d0388d7c9ded7c8fb9d3d2488c30ff29b1f037ac816e095ebe981a1e00fcde5e08bc29dfe
 MISC metadata.xml 355 BLAKE2B 2557fbd5c3427ccced7fc6d233954a3e9d4297c0bec17158997f4f7fb490b525235ae27fff1ed19113b596de77a23518505e20531c7e40020e3f54932f5d9e6f SHA512 9d9037805b94622cb468553fa27c948de2849ac4c6dc1eafae8c3261554b5e97b631fe77e4e589eff613822d316b2843bcab0c47547b202651c8a804a516554e
diff --git a/sci-biology/mira/mira-4.0.2.ebuild b/sci-biology/mira/mira-4.0.2.ebuild
index fd95fbfb2a78..f5ac6cfe70f5 100644
--- a/sci-biology/mira/mira-4.0.2.ebuild
+++ b/sci-biology/mira/mira-4.0.2.ebuild
@@ -81,7 +81,7 @@ src_configure() {
 #src_compile() {
 #	base_src_compile
 #	# TODO: resolve docbook incompatibility for building docs
-#	if use doc; then emake -C doc clean docs || die; fi
+#	use doc && emake -C doc clean docs
 #}
 
 src_install() {
diff --git a/sci-biology/mrbayes/Manifest b/sci-biology/mrbayes/Manifest
index a3a8a77c082f..89c72da46a5b 100644
--- a/sci-biology/mrbayes/Manifest
+++ b/sci-biology/mrbayes/Manifest
@@ -1,5 +1,4 @@
 AUX mb_readline_312.patch 1108 BLAKE2B 4413b4193ee7c0c51a1ad7a422474f137682151f932b28fc6ee98390a228a4e5bbabcf30f3d78fc56a79a665ffc40bf05376fbbf14b68ff43bc10a9001ec8e6e SHA512 0a169b8560853dbff87c983bf8220384dcf22f53106ce5711bf3b1fc76d8a9adbf1860618176dde65a8657abe3ad888521bf5485fc00d4014adf1acb7ba3f114
 DIST mrbayes-3.1.2.tar.gz 545968 BLAKE2B f4c5bbdde765fb9e596c17d5fd890b168c22cefb0d24b67c1c68623e1dcfa4df716a896fe120f7a1cac4234125b6ed524973506e47492ba3ec26e389783d618a SHA512 2fb0ee7224cbb69c1acf2ffb0c6c8974f63002cda4f39a626eadf80fad9cfc23861f8c03f5545970f3a81e02093d62b6a0549ab7d7f7080557e91e21b2c3ee14
-EBUILD mrbayes-3.1.2-r1.ebuild 1008 BLAKE2B c0523ef79227c24b5ede39bd9e262710ea7f4a408b20bef20e8f0dca0950b12e7d5171b901743c5a6e1fcec9089ce90c4e8385e1a3192e0fb7ab21195122f631 SHA512 5fcbdd396c7b035ecc0b596a9866fdc3544cf8993fd60efa0a5ab41f7cd4271c437626e3c131d9d07759cecef3cb8700a0b5b761ec87cbcbf12b9d206543f918
 EBUILD mrbayes-3.1.2-r2.ebuild 1347 BLAKE2B 6587af6372eff67641954301a26fd6b9bcb9bb5b1ba04fb4217da6a6686e71c166409a514c348c93334a5a191bcfdb96afe915f1edd93e5985380c314dce853c SHA512 c8655ecaf9933a963b072a242e44c156f89c635fae00fa135262911e2588beb623764a92634c27a16dcdac4fb70c16b88a428aa154a56ea816fd9b9ff2418037
 MISC metadata.xml 916 BLAKE2B 511d932eff0de935a1c8634cc6398bfe6cceb7f2766534e5486f5ff2aa4c900b8d48d7dabc5cee2506061c36421f0ef336f43b5df5d23a03ab5911a1fef87b1b SHA512 ab6be2e4111088bc13e6da5f65d11437dc05dbcdeab83e5d3899b913ff9ad3dc1f22ec81f2fe73f60bf991d01f0a8691eaa124ba24bd7ebb17d995fdd271bfef
diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild
deleted file mode 100644
index b67b4b228f9b..000000000000
--- a/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Bayesian Inference of Phylogeny"
-HOMEPAGE="http://mrbayes.csit.fsu.edu/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="debug mpi readline"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
-
-DEPEND="
-	sys-libs/ncurses
-	mpi? ( virtual/mpi )
-	readline? ( sys-libs/readline:0 )"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
-	use readline && epatch "${FILESDIR}"/mb_readline_312.patch
-	sed -e 's:-ggdb::g' -i Makefile || die
-}
-
-src_compile() {
-	local myconf mycc
-
-	if use mpi; then
-		mycc=mpicc
-	else
-		mycc=$(tc-getCC)
-	fi
-
-	use mpi && myconf="MPI=yes"
-	use readline || myconf="${myconf} USEREADLINE=no"
-	use debug && myconf="${myconf} DEBUG=yes"
-	emake \
-		OPTFLAGS="${CFLAGS}" \
-		LDFLAGS="${LDFLAGS}" \
-		CC=${mycc} \
-		${myconf}
-}
-
-src_install() {
-	dobin mb
-	insinto /usr/share/${PN}
-	doins *.nex
-}
diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest
index 25ed4df38bd1..45adecacdcf8 100644
--- a/sci-biology/ncbi-tools/Manifest
+++ b/sci-biology/ncbi-tools/Manifest
@@ -6,5 +6,5 @@ AUX ncbi-tools-extra_vib.patch 1393 BLAKE2B 3c9e0ffa614e7baccf87beea601561a8f6e1
 AUX ncbi-tools-lop.patch 701 BLAKE2B 9df2fd3ba86bc9a4f52d3c1809b4d795392666c601aa607d2377129c42562a99087387eaa69d9e9ae07545ea91808902db65718ccf3d671ca88f7255119b1028 SHA512 706dfb29f9b1eff1fcc7dc1df1d533563d9d12ead5b930930121ad92a3e8c159d1d7cf30acd9f4462772e8f27e6dcf45cd6125f2fa077b3902145f6faf1c8352
 AUX ncbirc 57 BLAKE2B 140c208cf1c7dbb6a204e58632c576e4edf0cd71d151b69f70839f1b06ae19db0d74d49179d2f0bc1320a40fabad49bed18a98a8bd2a75f6ecf068e647382c60 SHA512 0b9b68116b362ccc625623abf4e959abfb8555c31117216eefe3093fe2dd122c3ce508fe389c07a069d6f4322d889718e455de65dd3ab7d55a16d947ecb07cfd
 DIST ncbi-tools-2.2.26.tar.gz 68691452 BLAKE2B 21444227c6896c387f46a5490db1e4cf3ac437f94029c68f11ee3c5438bf2c34584d4b1b0ab18d3996f9c4e423a7e17fece510a96a1aa8be5dea6c5a2688f24c SHA512 da167216b56386b8c91a660e8ea0f3ac39b991d4519af9e02fc26aa16ed602eb3d9d874446f69a8f6840ae31a4d5a29da170e04e8a72b56f8c3ca038d1437014
-EBUILD ncbi-tools-2.2.26-r2.ebuild 4649 BLAKE2B 856db3d5f76ab1d246c8d67eb71b0c9c06f227cb88212ceafc0863370d52adc379135397dd8978cc57b2803f2cb8d36d53603dad5a8921616b8f236e9b47ff1e SHA512 c6611b3458c0369599c0027d9206d3dab72e52decae655d1f2b3394008d2dc96236c121754526c0f358bb3ed512ca7c485add1784bcd80e208f710330a3a208a
+EBUILD ncbi-tools-2.2.26-r2.ebuild 4612 BLAKE2B 817bb5d68cfda66ba62011a0e0cd627a1722942e748fc8e9d6fb93ae28a4088f7dfb95e291ff02e46251fa0732d82e6873b865cca29f9198f568b01a6ba9b81f SHA512 e9ee979f8a1daa5fdf2618235da187f666dfc04a20d7be61705df7d7f853190fbcd368878c5b5a7721af64535cba09d9a782b947652a86d69f758490af4ee9b9
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild
index 1d3b5784a3a1..2c59e13b5a97 100644
--- a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild
+++ b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild
@@ -114,7 +114,7 @@ src_install() {
 	dobin "${S}"/bin/*
 
 	for i in ${EXTRA_VIB}; do
-		dobin "${S}"/build/${i} || die "Failed to install binaries."
+		dobin "${S}"/build/${i}
 	done
 	use static-libs && dolib.a "${S}"/lib/*.a
 	mkdir -p "${ED}"/usr/include/ncbi
diff --git a/sci-biology/phylip/Manifest b/sci-biology/phylip/Manifest
index b51fe5eea178..74a149ca13f1 100644
--- a/sci-biology/phylip/Manifest
+++ b/sci-biology/phylip/Manifest
@@ -2,6 +2,6 @@ AUX README.Gentoo 643 BLAKE2B 95193d4c9c8fc8fb5796bb0a8ca470f440ac66eb1da9b9ed47
 DIST phylip-3.69.tar.gz 1511935 BLAKE2B 76aa5a79d2553c6f269c011f633d1101ee4d85ac398a36dd463e5605d90833ecb1e5f6c21edba3e142e2d4ab5ef034fa739e52e0ab3f941a7987915ae352be0b SHA512 e36d12bfe597896b4298c1d0e3b0b7bd783573dc03e861b9472d8284391b2339cb3fb58eb6580298724bbd516127b68925815455514f939da9272fcfed7e229d
 DIST phylip-3.696.tar.gz 3955721 BLAKE2B dc75fc442eb63e44bc2e68e5dc97b3ff8f741bfa53740ed57ca114b53dcb71db9baeb9a96c3e693f7fae92afbaa71c7b5acfb39e7770bacb6aafa8c33b355be6 SHA512 711a9a34be72b0f63c746733cd1384f091b7cc597dbd9a40c130e074efbf0a0ecc30e5a6b3452bb73dc69cddbdae2fc07d1c0a68f0be207471eab73ab876c6be
 EBUILD phylip-3.69-r1.ebuild 1145 BLAKE2B 55565e21aa748ede76c7c37fbc4cef8849707c1f7500ef283485f461ffc99282fca1316af634bf24abdb1ee33005d26e6dce1f2fe30d52c224882dbf3313ae8e SHA512 2f591f9616ab7ba831ea63eb02b8a83ab3ae0ed63221c02a59ad63f5d05475e2b51a4adccb47532740c809ee832cb0dd02e3389208d095c930e68070974e3fb3
-EBUILD phylip-3.696-r1.ebuild 1137 BLAKE2B 46e27a695491b597ccb6ee4f3e5fa33e44cfd322dc9a05856de06b9997dd698ae91ec6629eabe5684b17394c1026535d548da99d1ae76277bf5421dc505f426a SHA512 2c1141ada9169a1e399bd29c9ed8bea1ae1bca067dcdc557fbbecbd8f92695a1af5fd4299600cf7511971d2015da3156da180dc56d507e0ad2a9d445bb2ff1f4
-EBUILD phylip-3.696-r2.ebuild 1211 BLAKE2B ab783c32ca07e6b0a49696babc9527585277ab110138aecfde70e3d321b1de389580f4303a9ade1d4f379ee10dd75d4d6c0f5cc3193e99136321872ac1020150 SHA512 65347aa28dcb75f520030be9b0ab3ed349e01079b1ea3fcf5680f9a1da1fda08fc3464f099ecf6c05b9ef73b5f33f41e8d678eeaf4ce226585a7c186a6ba9a06
+EBUILD phylip-3.696-r1.ebuild 1130 BLAKE2B 94c4b4213d24b46fe60f3d180a1d8a742f9c173f5482e18e1521b0f3e61ac2738038c5a558fdbdeaece2f9887e08796d6981bc3ff54bec2e60dfb0ebffa7d156 SHA512 02e33c7a34910a006fb0e63d9cac40b9e71446b5b64185b968d46fdcb78217c4f2bdfe02b96ae2eefe10839e892c2c533581e9d149cfc63f1d64b2b87b1416a9
+EBUILD phylip-3.696-r2.ebuild 1204 BLAKE2B d6fcbe08f0528d657bc30da9c61c67571ee403c7f15caec8a86d2ed9a75958e471f8b2582d39c86f1ddb675636bf9d211665d398593651c968b9d87b9fac4a2a SHA512 2827584e9293a5bc95087c0d3f19b4d0ac1a7ecac6b5b81738abb16ee007d65ab91e14baf0885578afc4c369841456583d88ee51bf0738b3d04d4924eb086e5c
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/phylip/phylip-3.696-r1.ebuild b/sci-biology/phylip/phylip-3.696-r1.ebuild
index 3943d3637946..85150acaf9cb 100644
--- a/sci-biology/phylip/phylip-3.696-r1.ebuild
+++ b/sci-biology/phylip/phylip-3.696-r1.ebuild
@@ -42,7 +42,7 @@ src_install() {
 	mv exe/font* fonts || die "Font move failed."
 	mv exe/factor exe/factor-${PN} || die "Renaming factor failed."
 
-	dolib.so exe/*so && rm exe/*so || die
+	dolib.so exe/*so && rm exe/*so
 	dobin exe/*
 
 	dodoc "${FILESDIR}"/README.Gentoo
diff --git a/sci-biology/phylip/phylip-3.696-r2.ebuild b/sci-biology/phylip/phylip-3.696-r2.ebuild
index b3488d65421c..66391e0e662d 100644
--- a/sci-biology/phylip/phylip-3.696-r2.ebuild
+++ b/sci-biology/phylip/phylip-3.696-r2.ebuild
@@ -43,7 +43,7 @@ src_install() {
 	mv exe/font* fonts || die "Font move failed."
 	mv exe/factor exe/factor-${PN} || die "Renaming factor failed."
 
-	dolib.so exe/*so && rm exe/*so || die
+	dolib.so exe/*so && rm exe/*so
 	dobin exe/*
 
 	dodoc "${FILESDIR}"/README.Gentoo
diff --git a/sci-biology/plink/Manifest b/sci-biology/plink/Manifest
index d6102d8c41a6..8922b631e9c0 100644
--- a/sci-biology/plink/Manifest
+++ b/sci-biology/plink/Manifest
@@ -1,7 +1,3 @@
-AUX 1.07-flags.patch 1024 BLAKE2B 6b47f8782653d70eb86c4ebe7f06295f4b093fb17737b6ee9ab8f56fb02313049d5189ce0fa11d0ee8eb8d5c029f9d4432fb7aa0198282f56ba174bff2363b4f SHA512 6511b08ea740819e2d17bfc2168951f94d8b9ad1165b3ee0966bed8f7a4fe7fb313b9b32994d0405f613c14656125db736757fc7f2a2dd726db4c90e9a13dd6a
-AUX plink-1.07-gcc47.patch 1825 BLAKE2B 696f30be55c9fc26204041d255eea3c44675e51c1ad021fcfda105d40c04e312ac27514b297ed42d2c30bc2978a7d6a3a1bd29e44b9c0b1b186c496b2a4a6386 SHA512 dba53ba4e50bd2352ad2ed604570525b77bc5698259b12f618284c999efb776485e94485a1ad90b8cc1744a0aa004435f77ceb467e1fb9e475065e084938f7fe
-DIST plink-1.07-src.zip 2257297 BLAKE2B 572daeec24ec53daa017de9d4326c5db316f94fdcb40fb3d6a889643a5b5c60208a9424246e70414982a4659dd9c9bae5115d7ba3dc45183b521d1809fe2f00b SHA512 493f9f32ecd9eb20c5d11dc8ac98c47a9e695059cec3d1ad6f17465b71609577032368c0fee0d3d564e9451c3c07761e444717bec0f4628caefc587fceb1f6c3
 DIST plink-1.90_pre140514.zip 822157 BLAKE2B 3c29670862de99c9715bc37d8cffc2b02c0cb25ad746975f253ca1e8094b24668cc6739943c68bfa407471f30835a74c6ad027eaa56a92f13445e0a02854cad3 SHA512 679f1e136b11f35f1d49636bc44ffd17e72e4e38edc5daa270cd963ca39f7b8a80f31905a94de517059e5b3ea7a6bf518ae34a5c2af8a05c530bd6df771606c4
-EBUILD plink-1.07-r1.ebuild 1152 BLAKE2B 929aad0e5b3946e5b35f068b21c7549e22b7039dca8d053f8bd71d1fafa0171e093131a9b2591429184558438562ff8d1adaa4485e996b50f75f0e22ade7261a SHA512 eabbb86e94276de320007cc589407800ec29b1a850664c7d3ea74e2a3355a0528c28bf2c8cb416dbcba513e6dc2fe14df3cbfa0fe6678d1029815c62c1822f21
 EBUILD plink-1.90_pre140514.ebuild 1129 BLAKE2B ded7a69c8a040d4b4e2bcb2bb931adf6eeeccd6168d78dc7285322490f1744f7b4ae6c7e112e62a00ab0663227896cb3088c607a5a4a1d3903a080806618d6d7 SHA512 152653b04caa40c548108bb9cade22c968475faef8fd4af2627462928a6b2b364a8831bba569d467ff4a435e6fe76ce5d9862cb19da9565db1e9b974305fd0e4
-MISC metadata.xml 437 BLAKE2B a02d4418454b418b43b68ac394b2b08a196ca660d5b7cc5709e8750f6045f6a032700168bc5550557217f7af0f762ae7a4d24456ca3440e02674df6c604b161e SHA512 e4161118b7560456cca5ab5f14dfcf2cd3074e6be82dac3ce45b4ccd1d9d018c210d84ce29143c384618445e0a711ab47ed5450a25662dc762e871417c0f1dd4
+MISC metadata.xml 261 BLAKE2B 3768c926bca545090342a947ba83e706a8954c51b99a5e7b3476ba5198cd326fe1c3b8efb51dfd6be1800682556b8ceea065e388981463ab32f3d687951872f3 SHA512 537da0d3aa2741ebe4442d5dd9b53409decfc9d12ca8e5af8e737c4deb2910c884207e2d441025d19469816100889f04c11038bdffd6a1a15c6217495445090a
diff --git a/sci-biology/plink/files/1.07-flags.patch b/sci-biology/plink/files/1.07-flags.patch
deleted file mode 100644
index aa130f29beb2..000000000000
--- a/sci-biology/plink/files/1.07-flags.patch
+++ /dev/null
@@ -1,44 +0,0 @@
-diff --git a/Makefile b/Makefile
-index 172c795..466f09f 100644
---- a/Makefile
-+++ b/Makefile
-@@ -26,25 +26,25 @@ WITH_R_PLUGINS = 1
- WITH_WEBCHECK = 1
- FORCE_32BIT = 
- WITH_ZLIB = 1
--WITH_LAPACK = 
--FORCE_DYNAMIC = 
-+WITH_LAPACK = 1
-+FORCE_DYNAMIC = 1
- 
- # Put C++ compiler here; Windows has it's own specific version
- CXX_UNIX = g++
- CXX_WIN = c:\bin\mingw\bin\mingw32-g++.exe
- 
- # Any other compiler flags here ( -Wall, -g, etc)
--CXXFLAGS = 
-+CXXFLAGS ?= -O2
- 
- # Misc
--LIB_LAPACK = /usr/lib/liblapack.so.3
-+LIB_LAPACK = `$(PKG_CONFIG) --libs lapack`
- 
- 
- # --------------------------------------------------------------------
- # Do not edit below this line
- # --------------------------------------------------------------------
- 
--CXXFLAGS += -O3 -I.
-+CXXFLAGS += -I.
- OUTPUT = plink
- 
- # Some system specific flags
-@@ -151,7 +151,7 @@ OBJ = $(SRC:.cpp=.o)
- all : $(OUTPUT) 
- 
- $(OUTPUT) :
--	$(CXX) $(CXXFLAGS) -o $(OUTPUT) $(OBJ) $(LIB) 
-+	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(OUTPUT) $(OBJ) $(LIB) 
- 
- $(OBJ) : $(HDR)
- 
diff --git a/sci-biology/plink/files/plink-1.07-gcc47.patch b/sci-biology/plink/files/plink-1.07-gcc47.patch
deleted file mode 100644
index 6c289edae153..000000000000
--- a/sci-biology/plink/files/plink-1.07-gcc47.patch
+++ /dev/null
@@ -1,64 +0,0 @@
- elf.cpp    |    6 +++---
- idhelp.cpp |    8 ++++----
- sets.cpp   |    8 ++++----
- 3 files changed, 11 insertions(+), 11 deletions(-)
-
-diff --git a/elf.cpp b/elf.cpp
-index ec2ed3d..a57665f 100644
---- a/elf.cpp
-+++ b/elf.cpp
-@@ -1175,10 +1175,10 @@ void Plink::elfBaseline()
- 	  << setw(8) << gcnt << " "
- 	  << setw(8) << (double)cnt / (double)gcnt << "\n";
- 
--      map<int,int>::iterator i = chr_cnt.begin();
--      while ( i != chr_cnt.end() )
-+      map<int,int>::iterator j = chr_cnt.begin();
-+      while ( j != chr_cnt.end() )
- 	{
--	  int c = i->first;
-+	  int c = j->first;
- 	  int x = chr_cnt.find( c )->second;
- 	  int y = chr_gcnt.find( c )->second;
- 	  
-diff --git a/idhelp.cpp b/idhelp.cpp
-index a9244fa..8882097 100644
---- a/idhelp.cpp
-+++ b/idhelp.cpp
-@@ -772,12 +772,12 @@ void IDHelper::idHelp()
-       for (int j = 0 ; j < jointField.size(); j++ )
- 	{
- 	  set<IDField*> & jf = jointField[j];
--	  set<IDField*>::iterator j = jf.begin();
-+	  set<IDField*>::iterator k = jf.begin();
- 	  PP->printLOG(" { ");
--	  while ( j != jf.end() )
-+	  while ( k != jf.end() )
- 	    {
--	      PP->printLOG( (*j)->name + " " );
--	      ++j;
-+	      PP->printLOG( (*k)->name + " " );
-+	      ++k;
- 	    }
- 	  PP->printLOG(" }");
- 	}
-diff --git a/sets.cpp b/sets.cpp
-index 3a8f92f..66787e8 100644
---- a/sets.cpp
-+++ b/sets.cpp
-@@ -768,11 +768,11 @@ vector_t Set::profileTestScore()
-       //////////////////////////////////////////////
-       // Reset original missing status
- 
--      vector<Individual*>::iterator i = PP->sample.begin();
--      while ( i != PP->sample.end() )
-+      vector<Individual*>::iterator j = PP->sample.begin();
-+      while ( j != PP->sample.end() )
- 	{
--	  (*i)->missing = (*i)->flag;
--	  ++i;
-+	  (*j)->missing = (*j)->flag;
-+	  ++j;
- 	}
- 
-       ////////////////////////////////////////////////
diff --git a/sci-biology/plink/metadata.xml b/sci-biology/plink/metadata.xml
index c281934d9943..8417d1580d40 100644
--- a/sci-biology/plink/metadata.xml
+++ b/sci-biology/plink/metadata.xml
@@ -5,12 +5,4 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
-	<use>
-		<flag name="webcheck">
-			add support for online update checking every time the program starts
-		</flag>
-		<flag name="R">
-			add support R language
-		</flag>
-	</use>
 </pkgmetadata>
diff --git a/sci-biology/plink/plink-1.07-r1.ebuild b/sci-biology/plink/plink-1.07-r1.ebuild
deleted file mode 100644
index 3e1d4d5b0b43..000000000000
--- a/sci-biology/plink/plink-1.07-r1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Whole genome association analysis toolset"
-HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink/"
-SRC_URI="http://pngu.mgh.harvard.edu/~purcell/plink/dist/${P}-src.zip"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="lapack -webcheck R"
-KEYWORDS="amd64 x86"
-
-DEPEND="
-	app-arch/unzip
-	lapack? ( virtual/pkgconfig )"
-RDEPEND="
-	sys-libs/zlib
-	lapack? ( virtual/lapack )"
-
-S="${WORKDIR}/${P}-src"
-
-# Package collides with net-misc/putty. Renamed to p-link following discussion with Debian.
-# Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream.
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PV}-flags.patch \
-		"${FILESDIR}"/${P}-gcc47.patch
-	use webcheck || sed -i '/WITH_WEBCHECK =/ s/^/#/' "${S}/Makefile" || die
-	use R || sed -i '/WITH_R_PLUGINS =/ s/^/#/' "${S}/Makefile" || die
-	use lapack || sed -i '/WITH_LAPACK =/ s/^/#/' "${S}/Makefile" || die
-	tc-export PKG_CONFIG
-}
-
-src_compile() {
-	emake \
-		CXX_UNIX=$(tc-getCXX)
-}
-
-src_install() {
-	newbin plink p-link
-	dodoc README.txt
-}
diff --git a/sci-biology/psipred/Manifest b/sci-biology/psipred/Manifest
index cef1367df245..fa6d7469eacc 100644
--- a/sci-biology/psipred/Manifest
+++ b/sci-biology/psipred/Manifest
@@ -1,13 +1,9 @@
 AUX 3.1-Makefile.patch 1103 BLAKE2B ba9c5a7f60d62d66d1cd5a5e9b0a68ffe5c99124d02eae1924ffe92ecb2d24d7224e5bd0b37db3cf17da4f39d3c8b6b53e04466da8976e71910b9dcea9bc59ab SHA512 6e0daf4478b5b992ed1647bf653320b18cd2582ca69ebe761654bd4bd9c9c46b7de183ae84a28582cb5543603362eb7eb6c306ff562c3ec18c292d89480fd127
 AUX 3.1-path.patch 1128 BLAKE2B ea445427fe2ff574028b3d82ae353da5a1dfe3f5c7fade419287f6dc2e819471b4ec007dfee7cf71a1c958082a8dfa83acd5046208e0a7b16c07d90cdd68073f SHA512 e6201669db910f074bb13d1b781416d8d99300f328147cccd7755d5d6595b25aa45353f6da6566f225a067e94ab8ee41ea89bfd75cf2cdf2c076481707acf88c
 AUX 3.2-fgets.patch 427 BLAKE2B dba911ef9d28c230e38d326336fa7adfae31ffafd225d525968f58b1013df2f5812b0c678f37576714c7bfa396c7378b2e1201f8c6b2bea844c2e042eea7c0ec SHA512 a8a59a765057e20b9c606b8e4d76b5657a9a06150247b426d939805547148ddc8a1cb4282e04bcdcd756bfa6df7bebffcc77b84f62c86be2f643069d2ff913bb
-DIST psipred3.3.tar.gz 1239746 BLAKE2B b1afa9a6a85f239e02b5affec3a6ff48281f962b94b5b6e5c2f4da496a8f73b3d5103a3e77908976a6423eebcfc4e54d2bcb8f7ab012859a115d6f21d580e9d2 SHA512 38f5dd0f6eb6fc38888f9a850604b95904a8626d6862eb0b2a389caaf49af8f81436aa78a087da22281113d8afad2d28e5109ddade7d17718c1028eed8325b7e
 DIST psipred3.4.tar.gz 1102416 BLAKE2B 9797f4181357bb26455253370aca39857c39a2c4bcd521b10a139784e6fd5dc9e14b76c11d99989ac33c3a01fb62807957f9969daa5ac9d928b0b4e83e943743 SHA512 1bc7ac41a213766139324540ba6952538f2890749ecf217d771b4ce59e25231857d38c237ea573674f11a82300750e9a3ff628ec0156864863a9528a144cd919
 DIST psipred3.5.tar.gz 1101579 BLAKE2B 2fd86841cbc4bb86045b51f8283550832df8356ee88a6ef2c85281b5810debb23ac53652ddc5ffc9bd6f8e9e7248ce39ccee23400ff8fb49cd05b877d730b553 SHA512 a7b3f7d149f6a29cf0b48bdb900f6983d42af01132d8b54a7be88994d09fcf27dbe57115d41ec9654da6daf6898d5986d08fbdcefa3a4c81af0d358500cd40c2
-DIST psipred321.tar.gz 747151 BLAKE2B 8b58a2c45efc92e049622784e1ca39a622ecfb5f660554cf3a26ab9a7e85feb3e453935fca12f0a68328e5e736becdae737f80407730ea9315f4e79b19f71e8b SHA512 b742f5fd3151bd624452bf37761fa66d364ea5b28d9d005ae6ce6f52fc6f2b17df31d6f1e600bd6c57776a1812f22b1eafbca781b430811a010d74f157a75cd1
 DIST tdbdata.tar.gz 40241247 BLAKE2B c85a2fde9b29a14e1da27be1a7ea5fe1704f72b66cd79514dd50a3a0d2d8aab9341f7d5075f6d1896cefa54ca83948387b902b38780181777dc505a9a15b4aab SHA512 f96d7ffbb77e129251e27f62b7f099d944bacd14935e03fc52c9f0b262cce1ad477ad43520a93b407951fb8f5dd3ba2e27ff6b5ae8a637ec03bc02f8c7c3990c
-EBUILD psipred-3.2.1.ebuild 1077 BLAKE2B 9964a292420cf395be39b1757e591f2ca76f315c2fc6da8876a9339ec4e305815de1722c6eb4ba602242465a7754a2805159065d21417564c9b2e6fbc85bc127 SHA512 9906fa010d56bbc6b8f0967d4153272a400933ceca83c09e361290e6010d663d90d4099ccac85ed327948aca9f4e337ea839ac58dee97f50163768199b3bd7a0
-EBUILD psipred-3.3.ebuild 1174 BLAKE2B 4b0d3baa6fa748306bb32bea9bd397b4b8f1d009bc78253d4182ec66945b385734d1aa88fa561eef44336d9333e4e9c831c805fc677c7f51fc55a980456048dc SHA512 9a79023c9abbfe9b39243aae76192853ee7efde1bcbeb5a554e3014c86fca08e8f668b543e1c2894538dc37a76fea85755cb0edf871cefdc27db7377e216f7a3
-EBUILD psipred-3.4.ebuild 1191 BLAKE2B a9d1be16864e5bf05c73595648cc161ca508a8e8b6582a50aa76aeda971a4fd79daa5081569b7fc93b854afa9e119fa274befac8c32cbcbd331f3b722a717b41 SHA512 181b9c23a3263ca9febe3a78cfe207b65368d670abbc64b3d084584275d7bf56d0f87076b3ff2e7e9c9b5695145f9ad1e4759e62e090ec174477aab5321ff3fc
-EBUILD psipred-3.5.ebuild 1191 BLAKE2B a9d1be16864e5bf05c73595648cc161ca508a8e8b6582a50aa76aeda971a4fd79daa5081569b7fc93b854afa9e119fa274befac8c32cbcbd331f3b722a717b41 SHA512 181b9c23a3263ca9febe3a78cfe207b65368d670abbc64b3d084584275d7bf56d0f87076b3ff2e7e9c9b5695145f9ad1e4759e62e090ec174477aab5321ff3fc
+EBUILD psipred-3.4.ebuild 1215 BLAKE2B da6e40d6c96916d638aec4343a06be76705d0b0b729ab4332613e998539044780b76b94bdde12ebb01059ba1f5763c070dea0d13f2f1d934e1c3db1aaa4d2dab SHA512 8299f0b758e7192418794fcfaae2d81cc6b4f95dc0507b75b5aeac31c60318c9bfd7d0e9a307f23f163887ebe3af986b2c654d19e27bbf7d4111e56e46a1b649
+EBUILD psipred-3.5.ebuild 1215 BLAKE2B da6e40d6c96916d638aec4343a06be76705d0b0b729ab4332613e998539044780b76b94bdde12ebb01059ba1f5763c070dea0d13f2f1d934e1c3db1aaa4d2dab SHA512 8299f0b758e7192418794fcfaae2d81cc6b4f95dc0507b75b5aeac31c60318c9bfd7d0e9a307f23f163887ebe3af986b2c654d19e27bbf7d4111e56e46a1b649
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/psipred/psipred-3.2.1.ebuild b/sci-biology/psipred/psipred-3.2.1.ebuild
deleted file mode 100644
index 1bcb58744638..000000000000
--- a/sci-biology/psipred/psipred-3.2.1.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils prefix toolchain-funcs versionator
-
-MY_P="${PN}$(delete_all_version_separators)"
-
-DESCRIPTION="Protein Secondary Structure Prediction"
-HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/"
-SRC_URI="http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz"
-
-LICENSE="psipred"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-
-RDEPEND="
-	sci-biology/ncbi-tools
-	sci-biology/update-blastdb"
-DEPEND=""
-
-S="${WORKDIR}"
-
-src_prepare() {
-	rm -f bin/*
-	epatch \
-		"${FILESDIR}"/3.1-Makefile.patch \
-		"${FILESDIR}"/3.1-path.patch \
-		"${FILESDIR}"/3.2-fgets.patch
-	eprefixify runpsipred*
-}
-
-src_compile() {
-	emake -C src CC=$(tc-getCC)
-}
-
-src_install() {
-	emake -C src DESTDIR="${D}" install
-	dobin runpsipred* bin/* BLAST+/runpsipred*
-	insinto /usr/share/${PN}
-	doins -r data
-	dodoc README
-	newdoc BLAST+/README README-blast
-}
-
-pkg_postinst() {
-	elog "Please use the update_blastdb.pl in order to"
-	elog "maintain your own local blastdb"
-}
diff --git a/sci-biology/psipred/psipred-3.3.ebuild b/sci-biology/psipred/psipred-3.3.ebuild
deleted file mode 100644
index 4e0b0102837b..000000000000
--- a/sci-biology/psipred/psipred-3.3.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils prefix toolchain-funcs versionator
-
-#MY_P="${PN}$(delete_all_version_separators)"
-MY_P="${PN}${PV}"
-
-DESCRIPTION="Protein Secondary Structure Prediction"
-HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/"
-SRC_URI="
-	http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz
-	test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )"
-
-LICENSE="psipred"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-
-RDEPEND="
-	sci-biology/ncbi-tools
-	sci-biology/update-blastdb"
-DEPEND=""
-
-S="${WORKDIR}"/${PN}
-
-src_prepare() {
-	rm -f bin/*
-	epatch \
-		"${FILESDIR}"/3.1-Makefile.patch \
-		"${FILESDIR}"/3.1-path.patch \
-		"${FILESDIR}"/3.2-fgets.patch
-	eprefixify runpsipred*
-	emake -C src clean
-}
-
-src_compile() {
-	emake -C src CC=$(tc-getCC)
-}
-
-src_install() {
-	emake -C src DESTDIR="${D}" install
-	dobin runpsipred* bin/* BLAST+/runpsipred*
-	insinto /usr/share/${PN}
-	doins -r data
-	dodoc README
-}
-
-pkg_postinst() {
-	elog "Please use the update_blastdb.pl in order to"
-	elog "maintain your own local blastdb"
-}
diff --git a/sci-biology/psipred/psipred-3.4.ebuild b/sci-biology/psipred/psipred-3.4.ebuild
index d1d6a547d17f..1fe4c6dced52 100644
--- a/sci-biology/psipred/psipred-3.4.ebuild
+++ b/sci-biology/psipred/psipred-3.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -18,6 +18,7 @@ LICENSE="psipred"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="test"
+RESTRICT="!test? ( test )"
 
 RDEPEND="
 	app-shells/tcsh
diff --git a/sci-biology/psipred/psipred-3.5.ebuild b/sci-biology/psipred/psipred-3.5.ebuild
index d1d6a547d17f..1fe4c6dced52 100644
--- a/sci-biology/psipred/psipred-3.5.ebuild
+++ b/sci-biology/psipred/psipred-3.5.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -18,6 +18,7 @@ LICENSE="psipred"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="test"
+RESTRICT="!test? ( test )"
 
 RDEPEND="
 	app-shells/tcsh
diff --git a/sci-biology/repeatmasker/Manifest b/sci-biology/repeatmasker/Manifest
index bb8698101fac..9bcd96590519 100644
--- a/sci-biology/repeatmasker/Manifest
+++ b/sci-biology/repeatmasker/Manifest
@@ -1,3 +1,3 @@
 DIST RepeatMasker-open-4-0-1.tar.gz 84077910 BLAKE2B 45598d46ef1c0e1233ed5ce10c2d29e4b2ef1a6843846970df2d0f997a22657eeed7dd7c851418d6f751468b22327b47f3b72105fdcfa56bbebe97395946ab37 SHA512 6b710a02b2964bca6acb25cc918bd56f7caba7b80b3b683972f0584180bf0fd3704f657d7ee341187a4ac86d9883e62eb4f09da237fa8ef1b481137d1a89963e
-EBUILD repeatmasker-4.0.1.ebuild 1529 BLAKE2B 3cf4337be1db71be2a69f3455ae5d6c7ced9fb213f1020ef633ce97b9c7a63378229fe87cf5f7e1698c52d3d478cc6e480683ed0391278e09cb5d27631772591 SHA512 72c2663f3c614e476f23d880551c6f78fcc239c56905726c90663a467af22ad42cb4518667c2a1301f55230d890b390967a5799bb4460c4d0e9909bc2d5c5bd3
+EBUILD repeatmasker-4.0.1.ebuild 1501 BLAKE2B c8a6bef25b5e9cfbf4be2d5336b7b9960872c16368c470dd720be2a76529e894077ee2875999cfbce66b954f3ec059de0a9e98e605e3c4b17338f520a43580f2 SHA512 a90a31bd066e05384f6583a04f2e8bb4624f84e2125b25eebc3b253ceca1e9bf1090e11ddbdda824f1e9a939b4fbe8f900335e14c6604d1f947ab6083191df5d
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild
index 41c28eb17f4e..bf6097df1f68 100644
--- a/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild
@@ -42,16 +42,16 @@ Y
 src_install() {
 	exeinto /usr/share/${PN}
 	for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do
-		doexe $i || die
-		dosym /usr/share/${PN}/$i /usr/bin/$i || die
+		doexe $i
+		dosym /usr/share/${PN}/$i /usr/bin/$i
 	done
 
 	dodir /usr/share/${PN}/lib
 	insinto /usr/share/${PN}/lib
-	doins "${S}"/*.pm || die
+	doins "${S}"/*.pm
 
 	insinto /usr/share/${PN}
-	doins -r util Matrices Libraries taxonomy.dat *.help || die
+	doins -r util Matrices Libraries taxonomy.dat *.help
 	keepdir /usr/share/${PN}/Libraries
 
 	dodoc README INSTALL *.help
diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest
index 58feb9437819..12365d2c556e 100644
--- a/sci-biology/seqan/Manifest
+++ b/sci-biology/seqan/Manifest
@@ -6,8 +6,8 @@ AUX seqan.pc.in 263 BLAKE2B ffd2a2c1ac74af7bc6b33c5959792551447ee61fe87fbb8bc696
 DIST seqan-src-1.4.2.tar.gz 120601994 BLAKE2B 62de2f961ba3c7c564090d746877d2b0b94ec7967c56f28786a286160770e66f0a8f08aacbe76d828cf429f92f0aa640ab29f5220297686979df9b7e9f9a0408 SHA512 dbb56167c507b70111619a414054d9e70f1db42507bbfdf9e40c5dcbbe9489ad4187d882e638a675e96551c860c08f8203c929c4c9a558b19ea7d6059f50492a
 DIST seqan-src-2.2.0.tar.gz 110936119 BLAKE2B be41f266e140ec5992f7e9e507659dc7902aad0e0dd17e6a8c6c9ef0b11f690454a771ba10a5998ccf70e2e50ef9b24904ebf537d982b2cbc68963c004097614 SHA512 1097372976ec9c86baa3787ac38aa4fde3a3e153d81c22435e6a12df87d8063165f27406de33851bffadd904b0ac4ea579a28625cff6257fe8c14d906f408421
 DIST seqan-v2.4.0.tar.gz 109626901 BLAKE2B a10b5ee9a95667f560a8c2aec3808131f5f838f3c07d56584f4b29e9622912bf3d00b958b02db7c9d62dd52d9d08a171abcccef7f50cddf0407538168cf2c592 SHA512 f92cfc97304581920850c5d49fe4336f7c3855e99c3bcb035b6172fa7307e08e6f06fb06d1cd8f5b447c3220fc7f669684fbfe25641b43e9f6953999cf9ddd4b
-EBUILD seqan-1.4.2-r1.ebuild 1973 BLAKE2B 609d230907439c3616884946437ec066d38839fb7163c76baa2123b50e960ff716fa88dfe2c70670aa754db5119611c8563c4db0ffe32b1ef500ad24f714bf4e SHA512 ae79e4dc1ad47ec9c23e113921efcb5afceeac010b0c576a30faede932ffbcb1f74c2b87a5109142601af20be8e3c794643c14ac8ed5c99675657a5e220954b0
-EBUILD seqan-2.2.0-r1.ebuild 2679 BLAKE2B 54698806cd7912ad28089c47ccea9f660a1a641a7a31ba9e8c48cb596d96ef89b22f85ce2c46ed22674956b94087427a8196b5d7462bd05b31951b06b61e4858 SHA512 e0dd151d5212ce3f4cb30f5454e68d4f8b61bb760cbc1bb003a6f302989f9edb7e32bce86eb84a265160b7534a5039eb7ef3abdff1baa61e6c4c0d9ddb572614
+EBUILD seqan-1.4.2-r1.ebuild 1997 BLAKE2B 7e7934e70e17b65cc3557dc2f9e7c7d16db4f57bee1b0238d211ed57039e47cc03f495dc068e94d5d4502983c0d0e3b4cca21c0e88ff6c63a9e4d1496ba2850d SHA512 b1ba7611fe3de91484b05e06e4313eb7422bf38d5987c164e9ae7b788b4e7c3cdc0cd5702c215bd6747d2dd94f305f9ae8ea359699e5c32114e8a03514007bfd
+EBUILD seqan-2.2.0-r1.ebuild 2703 BLAKE2B e56cdb3ad4cf674e2349a8d380b49c58b68b528ae28e7b52066a24cf09efbc262855d51f8f3a6ae8111e46b3f95bcec8eaa117a43a895c5bca59963769300307 SHA512 e9524b59db85d13554f99b01c681e2d9137d8971a7df628c2a0b7f5774f8ea324191b3ed6bf0c51b8023b7b1947586adad22709c959656cf1fda58c92c3d89a6
 EBUILD seqan-2.4.0.ebuild 1917 BLAKE2B c53b1c51fd7b8a1c1498f5b2072f26a7829545f626fef177e0e64bc488784f7b9273c2f101db4c045203b3198aa6f37fa6f3226c633575815fbb95174ed5d30a SHA512 6f17b5d2d3be7a19fadcad798f0328fe467bc811d0a931c7b43df87fe23d17ebf2fb48aa197b838c9756bf9f3af7eaa04d346b0b5a05b03b28d03e4e80400c71
 EBUILD seqan-9999.ebuild 1860 BLAKE2B 745e69b7a80868f3faf45a6dfc9727835c8482737b3902a9e0f809a456ce5b3335d821d1106579da01fa495bc3df1caf222f425e41e172479b7de4e4a6e6a2b4 SHA512 3da317388c84933b817705825385c20c3673208c9a3fa1867078f7aea6a9959c6db3b8463cc3713d728180e30093cb1e30220072866305ac58f7b3de6b412f83
 MISC metadata.xml 372 BLAKE2B d620401f1aab9be80ddb6dc7abe737fd3e6322c560136e2c3b33d9246beca2986b4d91225b506e8c3035550994c3f714a11c0d8b17efd30c29278002d4eb7a12 SHA512 ae6c49e7e45c0ce4dd4fe27d21c5376c6fb8d7bfd2f98b7775f4689811680fa92c0b71ac0db70f6969660c4aee344f710ef752a467d6d46dd83aa47386d2ec17
diff --git a/sci-biology/seqan/seqan-1.4.2-r1.ebuild b/sci-biology/seqan/seqan-1.4.2-r1.ebuild
index b06c697334c5..3a7f55c710c3 100644
--- a/sci-biology/seqan/seqan-1.4.2-r1.ebuild
+++ b/sci-biology/seqan/seqan-1.4.2-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -15,6 +15,7 @@ SLOT="$(get_version_component_range 1-2)"
 LICENSE="BSD GPL-3"
 KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
 IUSE="cpu_flags_x86_sse4_1 test"
+RESTRICT="!test? ( test )"
 REQUIRED_USE="cpu_flags_x86_sse4_1"
 
 RDEPEND="
diff --git a/sci-biology/seqan/seqan-2.2.0-r1.ebuild b/sci-biology/seqan/seqan-2.2.0-r1.ebuild
index b559386860d2..5e139cd7e601 100644
--- a/sci-biology/seqan/seqan-2.2.0-r1.ebuild
+++ b/sci-biology/seqan/seqan-2.2.0-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -15,6 +15,7 @@ SLOT="0"
 LICENSE="BSD GPL-3"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="cpu_flags_x86_sse4_1 doc test"
+RESTRICT="!test? ( test )"
 REQUIRED_USE="cpu_flags_x86_sse4_1"
 
 RDEPEND="
diff --git a/sci-biology/shrimp/Manifest b/sci-biology/shrimp/Manifest
index c1e3472dfb7e..6a5d38227ddb 100644
--- a/sci-biology/shrimp/Manifest
+++ b/sci-biology/shrimp/Manifest
@@ -1,5 +1,3 @@
-DIST SHRiMP_2_0_1.src.tar.gz 158535 BLAKE2B 85b5462e812bece6a9ad51044bfeb823082e41ee66f313e0f7f621a29bfe5384d640278fa90ac102f476bef1538b0c7e1965dae7c1b877426b0d16f147a1e6ac SHA512 1cb5d46d59102502acb26c33f1d5537644268704145f6e2ae7428aeaba6681cf1e63f7924d8ee696431675f2c4627da46fd0171f25bbb3296d247339c2d709eb
 DIST SHRiMP_2_2_3.src.tar.gz 4596867 BLAKE2B 64e485b8e2524062c11c581bbcac426800c9f42f61da467378dbfd3add63f721a9da9c04df61bde3704e654a20395e799e89fc5e47129b1d3f5bc93f960470fa SHA512 029179aeeb317194b998c29aa91d1d2ce5ccbc6f9ad4a1043d1e5fc75d3344c2f39500ab07e8389c09fa179f0c9b59afee22691bc4eb5d396777f4e0fe25f2d5
-EBUILD shrimp-2.0.1.ebuild 1279 BLAKE2B f6606ff9c467de94228185c483db4da8d02784a5cfb0c8c1ce93ff56971e257836470c202bbeb2f85e598e3881bba81153448d5e9604bebe065110f54b8cb8fc SHA512 d16226d78b627809be5dc8b5fb39e552a71ceb6a8834ad68650fd9d3c69b425ee2e29a56f1e9b1b59e56f43a149169cc75c6694fe35c18ebc052fa7d30b6902d
 EBUILD shrimp-2.2.3.ebuild 1818 BLAKE2B 4878f0ce5782f0bc5fb5d4b14d5d713f21268b612cb18a2f14e19e3cca1c2270940b1f74220da0788fea9e142c803bcc77b9b2c04479a9432f06b9b29f3f7705 SHA512 2bfdb6f1cf7678dc9fafd66c25c07f55671f39600a44c606bac33652806105ff448d231202fb405307a0a49716557aa7cc63d371163821af2d919422ff9e2e6f
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/shrimp/shrimp-2.0.1.ebuild b/sci-biology/shrimp/shrimp-2.0.1.ebuild
deleted file mode 100644
index c71aa047c1a7..000000000000
--- a/sci-biology/shrimp/shrimp-2.0.1.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit flag-o-matic toolchain-funcs
-
-MY_PV=${PV//./_}
-
-DESCRIPTION="SHort Read Mapping Package"
-HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/"
-SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz"
-
-LICENSE="shrimp"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE="custom-cflags"
-
-# file collision on /usr/bin/utils #453044
-DEPEND="
-	!sci-biology/emboss
-	!sci-mathematics/cado-nfs"
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}/SHRiMP_${MY_PV}
-
-pkg_setup() {
-	if [[ ${CC} == *gcc* ]] &&	! tc-has-openmp; then
-		elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc"
-		die "C compiler lacks OPENMP support"
-	fi
-}
-
-src_prepare() {
-	sed -e '1 a #include <stdint.h>' -i common/dag_glue.cpp || die
-	# respect LDFLAGS wrt 331823
-	sed -i -e "s/LDFLAGS/LIBS/" -e "s/\$(LD)/& \$(LDFLAGS)/" \
-		-e 's/-static//' Makefile || die
-}
-
-src_compile() {
-	append-flags -fopenmp
-	use custom-cflags || append-flags -O3 # per instructions in BUILDING
-	tc-export CXX
-	emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	rm bin/README
-	dobin bin/*
-	insinto /usr/share/${PN}
-	doins -r utils
-	dodoc HISTORY README TODO SPLITTING_AND_MERGING
-}
diff --git a/sci-biology/tree-puzzle/Manifest b/sci-biology/tree-puzzle/Manifest
index 2a82bc13aa0d..4805dbe3df20 100644
--- a/sci-biology/tree-puzzle/Manifest
+++ b/sci-biology/tree-puzzle/Manifest
@@ -1,4 +1,4 @@
 AUX tree-puzzle-impl-dec.patch 380 BLAKE2B 22c00e2e0b4682a98212ec0b6e941ac37eff4cdeb8f684dc607e80a1617a35e209d23ac739af0e69af91deb8122fe04c3f9e7bdbd0c54edd8e603a817bdf0848 SHA512 092743fff8a305a41ef55afde3e058c1892d9c608bd05cb87de38a451c2b9cafc7749825347d5c245f1c6b1e84cf9d28b63bd4e7389440da5604766412290110
 DIST tree-puzzle-5.2.tar.gz 875142 BLAKE2B aa13e9a7aa403c12aebefb94a1931baa8b17cbee56d20011cb06db5a7b1b7f78c719ed6c6bfb0b79e47dc652d7b984415694907fc6cd56bdbe9eebca4aaa96a8 SHA512 5b9a729b120cba59f59ba426acd439cf396826ea01e75361b23387ccb9baf295d2512f21af96071a5f7b7507db4ff4d6b135cf6c5b6233a8b438532d31abe751
-EBUILD tree-puzzle-5.2.ebuild 1355 BLAKE2B 4d9dd7728bc34b4481d9b63030618b343f6cdec04cf24670be81319c8a9e2e7f7ce42956797dc51da24e1e42e9e5dd7a20be018f027a04f38cb55b850d1c5a34 SHA512 44c268b736aa1769c4b85170094d620bdd12798e8d194d4d991f5a2078641d29a19216bb733636052337b93863dec386b0cf2bc3544401059c566205d6d5fe7d
+EBUILD tree-puzzle-5.2.ebuild 1290 BLAKE2B e02eee43fabed81ca8d164630aa720365eb1cdab5660b878a750138b4dbdda42e3d04da4b0f3f404b45852e26c5ec56f005aa54cedfdf63d4e98718b2f0be145 SHA512 fa04a780ca5680424507123a007856fd442245812b03621efb29215bb8b651d19d5874904a6f4791d446f95f97cee676c2ac33554d4b893ed7068e3ecb70eb1e
 MISC metadata.xml 1555 BLAKE2B afe1aecc51f612aad5b1fd991ba020fe15cf5336c0cd521330394ef486a786e088f8a85d0b89944f75557109c56409709e92d62bbde67f8f1f41ef015dcf3bc9 SHA512 d74b3243cb62071c16a1728cb14e4c226644b8116dc032ac2d74a928260a252334583d1867ec3663533f36fa1bb746270f1d33f6fb4bae220af86eba668307b8
diff --git a/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild
index 27dd0bc2212f..8e2a07f8183e 100644
--- a/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild
+++ b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=4
+EAPI=7
 
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="Maximum likelihood analysis for nucleotide, amino acid, and two-state data"
 HOMEPAGE="http://www.tree-puzzle.de"
@@ -13,44 +13,41 @@ LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos"
 IUSE="mpi"
+RESTRICT="test"
 
 DEPEND="mpi? ( virtual/mpi )"
 RDEPEND="${DEPEND}"
 
-RESTRICT="test"
-
-pkg_setup () {
-	use mpi && [ $(tc-getCC) = icc ] && die "The parallelized version of tree-puzzle cannot be compiled using icc.
-	Either disable the \"mpi\" USE flag to compile only the non-parallelized
-	version of the program, or use gcc as your compiler (CC=\"gcc\")."
-}
+PATCHES=( "${FILESDIR}"/${PN}-impl-dec.patch )
 
-src_prepare() {
-	epatch "${FILESDIR}"/${PN}-impl-dec.patch
+pkg_setup() {
+	use mpi && [[ $(tc-getCC) == icc* ]] &&
+		die "The parallelized version of tree-puzzle cannot be compiled using icc.
+			Either disable the \"mpi\" USE flag to compile only the non-parallelized
+			version of the program, or use gcc as your compiler (CC=\"gcc\")."
 }
 
 src_configure() {
 	default
 
 	if ! use mpi; then
-			sed \
-				-e 's:bin_PROGRAMS = puzzle$(EXEEXT) ppuzzle:bin_PROGRAMS = puzzle :' \
-				-e 's:DIST_SOURCES = $(ppuzzle_SOURCES) $(puzzle_SOURCES):DIST_SOURCES = $(puzzle_SOURCES):' \
-				-i "${S}"/src/Makefile || die
+		sed \
+			-e 's:bin_PROGRAMS = puzzle$(EXEEXT) ppuzzle:bin_PROGRAMS = puzzle :' \
+			-e 's:DIST_SOURCES = $(ppuzzle_SOURCES) $(puzzle_SOURCES):DIST_SOURCES = $(puzzle_SOURCES):' \
+			-i src/Makefile || die
 	fi
 }
 
 src_install() {
 	dobin src/puzzle
 	use mpi && dobin src/ppuzzle
-	dodoc AUTHORS ChangeLog README
+	einstalldocs
 
 	# User manual
-	insinto /usr/share/doc/${PF}
-	doins doc/tree-puzzle.pdf
+	dodoc doc/tree-puzzle.pdf
 
 	# Example data files
 	insinto /usr/share/${PN}/data
-	rm data/Makefile*
-	doins data/*
+	rm data/Makefile* || die
+	doins -r data/.
 }
diff --git a/sci-biology/velvet/Manifest b/sci-biology/velvet/Manifest
index 88cc05d2f45e..40f51b903d70 100644
--- a/sci-biology/velvet/Manifest
+++ b/sci-biology/velvet/Manifest
@@ -1,6 +1,3 @@
-AUX velvet-1.0.18-gentoo-r1.diff 7879 BLAKE2B a1aaa683c82d7c69669c815b2b3351ba115fddb600fe0eea46d2cc002b75b752565ed9e289c2f0143550e5ffcea13587bb8f8cb31227d38ed63a769da3b05b88 SHA512 7aa112850c1d83220e1545ef29aa3e445ce55bc4334d062c353a5c5681723a3492c8dec52aeb58cfb5d464d1c748b721dc6400509fa872a48c428a2e0f9cdbf0
-DIST velvet_1.0.18.tgz 7598196 BLAKE2B acaee0fef39afe34d80a6be0bcb0069fd2daab396741034fc9d298a3a828303dcba50f2cd40d94f2b97f5066b281df810716f548cd88a64ae2c661ad3e012c1f SHA512 6823265bae085df85513f29e0ac5f17951de4d39aa62bce205f1b1579e274c08047360f25f1936c89361281f66b8a4b755f611890a6a98c02751c74e69ae03ad
 DIST velvet_1.2.10.tgz 18818559 BLAKE2B 5723c9c040e570cd88b774e5b0044dd04def88778fe2b137ec7c007ab83fc98e5423ad1d9d0499780cf6d3152347ca1a4e4e6b6c1900ce4adfc4930f1f6d3c34 SHA512 a6f3e35cebceb22cc10e83088b8cd9758492da78866237cae63d8826d6f5cfb44d82dd8bfcb1185d37cd434d4c7a0f2ac7135bb80a51db86e754afd6156ea874
-EBUILD velvet-1.0.18-r1.ebuild 1506 BLAKE2B 53b3c71ae3cf401f5626215b418c15ac4dbc96817bbadf127dbc2739d6686a8a227ec61f5112a0aff444d4fee53ed5513042c78c28c3a8086158c249f43040f4 SHA512 13551819ee7eb7a86dd388a31cd48688fabced7cd42cfbdb536615c314ea9da5a94fb1fd4a52695c8a931c62407991592948f53a2d191133a6d394d15c2708c2
 EBUILD velvet-1.2.10.ebuild 2106 BLAKE2B d7ea6a576303cffaf8785fc125b6848d3dde0775756867c952d196f0f1e55959e5d7a3b29c0096108208db043658d5f7e382e3ef701b20c4c6a383cc3f561934 SHA512 6c02607cd77b12cd2a64a92cc2a469994aba906823b3acf5c36537749a6268e8766bbc4e319d057430204af1ae36c9351f68ff579d4065048851fac9e12ccc3b
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/velvet/files/velvet-1.0.18-gentoo-r1.diff b/sci-biology/velvet/files/velvet-1.0.18-gentoo-r1.diff
deleted file mode 100644
index ed53a1229b5b..000000000000
--- a/sci-biology/velvet/files/velvet-1.0.18-gentoo-r1.diff
+++ /dev/null
@@ -1,72 +0,0 @@
-diff -durr Makefile Makefile
---- Makefile	2011-01-27 16:52:58.853408562 +0000
-+++ Makefile	2011-01-27 17:01:45.088065521 +0000
-@@ -1,8 +1,4 @@
--CC = gcc
--CFLAGS = -Wall
--DEBUG = -g
--LDFLAGS = -lm
--OPT = -O3
-+LIBS = -lm -lz
- MAXKMERLENGTH=31
- CATEGORIES=2
- DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
-@@ -41,29 +37,29 @@
- 	-rm obj/*.o obj/dbg/*.o 
- 
- zlib : 
--	cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
-+	echo "unbundled zlib"
- 
- velveth : obj 
--	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(Z_LIB_FILES)
-+	$(CC) $(CFLAGS)  $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(LIBS) 
- 
- 
- velvetg : obj
--	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES)
-+	$(CC) $(CFLAGS)  $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(LIBS)
- 
- debug : override DEF := $(DEF) -D DEBUG 
- debug : cleanobj obj/dbg
--	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
--	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS) 
-+	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS) 
- 
- color : override DEF := $(DEF) -D COLOR
- color : cleanobj obj_de
--	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES)
--	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES)
-+	$(CC) $(CFLAGS)  $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(LIBS) 
-+	$(CC) $(CFLAGS)  $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(LIBS) 
- 
- colordebug : override DEF := $(DEF) -D COLOR -D DEBUG
- colordebug : cleanobj obj/dbg_de
--	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
--	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS) 
-+	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS) 
- 
- objdir:
- 	mkdir -p obj
-@@ -83,7 +79,7 @@
- obj/dbg_de: zlib cleanobj obj/dbgdir $(OBJDBG)
- 
- obj/%.o: src/%.c
--	$(CC) $(CFLAGS) $(OPT) $(DEF) -c $? -o $@ 
-+	$(CC) $(CFLAGS)  $(DEF) -c $? -o $@ 
- 
- obj/dbg/%.o: src/%.c
- 	$(CC) $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@ 
-diff -durr src/readSet.c src/readSet.c
---- src/readSet.c	2011-01-27 16:52:58.804084948 +0000
-+++ src/readSet.c	2011-01-27 17:02:55.380324786 +0000
-@@ -24,6 +24,7 @@
- #include <math.h>
- #include <time.h>
- #include <limits.h>
-+#include <zlib.h>
- 
- #include "globals.h"
- #include "tightString.h"
diff --git a/sci-biology/velvet/velvet-1.0.18-r1.ebuild b/sci-biology/velvet/velvet-1.0.18-r1.ebuild
deleted file mode 100644
index a8ec87b6625a..000000000000
--- a/sci-biology/velvet/velvet-1.0.18-r1.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils toolchain-funcs flag-o-matic
-
-MY_P=${PN}_${PV}
-
-DESCRIPTION="A sequence assembler for very short reads"
-HOMEPAGE="https://www.ebi.ac.uk/~zerbino/velvet/"
-SRC_URI="https://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="-doc"
-KEYWORDS="amd64 x86"
-
-RDEPEND="sys-libs/zlib"
-DEPEND="${RDEPEND}
-	doc? ( virtual/latex-base )"
-
-S="${WORKDIR}"/${MY_P}
-
-src_prepare() {
-	# necessary?
-	# append-flags -O3 # as recommended by upstream
-	epatch "${FILESDIR}"/${P}-gentoo-r1.diff
-	use doc || sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
-}
-
-src_compile() {
-	tc-export CC
-	MAKE_XOPTS=""
-	if [[ $VELVET_MAXKMERLENGTH != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS MAXKMERLENGTH=$VELVET_MAXKMERLENGTH"; fi
-	if [[ $VELVET_CATEGORIES != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS CATEGORIES=$VELVET_CATEGORIES"; fi
-	emake -j1 $MAKE_XOPTS || die
-	emake -j1 $MAKE_XOPTS color || die
-}
-
-src_install() {
-	dobin velvet{g,h,g_de,h_de} || die
-	insinto /usr/share/${PN}
-	doins -r contrib || die
-	dodoc Manual.pdf CREDITS.txt ChangeLog || die
-}
-
-pkg_postinst() {
-	elog "To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual,"
-	elog "please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your"
-	elog "environment or /etc/portage/make.conf, then re-emerge the package. For example:"
-	elog "	VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
-}